chr11-2909364-CG-C

Variant names:

• chr11-2909364-CG-C
• rs67769451
• NM_002555.6:c.403+14delG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_002555.6(SLC67A1):​c.403+14delG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 1.0 (75975 hom., cov: 0)
  • Exomes 𝑓: 1.0 (681699 hom.)
• Consequence: SLC67A1 NM_002555.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.00600
• Publications: 5 publications found

Genes affected

SLC67A1 (HGNC:10964): (solute carrier family 22 member 18) This gene is one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. This gene is imprinted, with preferential expression from the maternal allele. Mutations in this gene have been found in Wilms' tumor and lung cancer. This protein may act as a transporter of organic cations, and have a role in the transport of chloroquine and quinidine-related compounds in kidney. Several alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Oct 2015]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 11-2909364-CG-C is Benign according to our data. Variant chr11-2909364-CG-C is described in ClinVar as Benign. ClinVar VariationId is 768418.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002555.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC67A1	NM_002555.6	MANE Select	c.403+14delG		intron	N/A	NP_002546.3
	SLC67A1	NM_001315501.2		c.658+14delG		intron	N/A	NP_001302430.1
	SLC67A1	NM_183233.3		c.403+14delG		intron	N/A	NP_899056.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC67A1	ENST00000649076.2	MANE Select	c.403+14delG		intron	N/A	ENSP00000497561.1	Q96BI1
	SLC67A1	ENST00000347936.6	TSL:1	c.403+14delG		intron	N/A	ENSP00000307859.2	Q96BI1
	SLC67A1	ENST00000380574.5	TSL:1	c.403+14delG		intron	N/A	ENSP00000369948.1	Q96BI1

Frequencies

GnomAD3 genomes AF: 0.999 AC: 151925 AN: 152012 Hom.: 75919 Cov.: 0

Gnomad AFR AF: 1.00

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.998

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.999

GnomAD2 exomes AF: 0.999 AC: 116563 AN: 116642 AF XY: 0.999

Gnomad AFR exome AF: 1.00

Gnomad AMR exome AF: 0.998

Gnomad ASJ exome AF: 0.999

Gnomad EAS exome AF: 1.00

Gnomad FIN exome AF: 1.00

Gnomad NFE exome AF: 0.999

Gnomad OTH exome AF: 0.999

GnomAD4 exome AF: 0.999 AC: 1364523 AN: 1365656 Hom.: 681699 Cov.: 0 AF XY: 0.999 AC XY: 672778 AN XY: 673294

African (AFR) AF: 1.00 AC: 29296 AN: 29300

American (AMR) AF: 0.998 AC: 33589 AN: 33662

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 24389 AN: 24408

East Asian (EAS) AF: 1.00 AC: 34083 AN: 34084

South Asian (SAS) AF: 1.00 AC: 77401 AN: 77402

European-Finnish (FIN) AF: 1.00 AC: 34448 AN: 34448

Middle Eastern (MID) AF: 1.00 AC: 4086 AN: 4086

European-Non Finnish (NFE) AF: 0.999 AC: 1070386 AN: 1071380

Other (OTH) AF: 0.999 AC: 56845 AN: 56886

GnomAD4 genome AF: 0.999 AC: 152037 AN: 152124 Hom.: 75975 Cov.: 0 AF XY: 1.00 AC XY: 74322 AN XY: 74358

African (AFR) AF: 1.00 AC: 41529 AN: 41534

American (AMR) AF: 0.998 AC: 15253 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3470 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5122 AN: 5122

South Asian (SAS) AF: 1.00 AC: 4830 AN: 4830

European-Finnish (FIN) AF: 1.00 AC: 10607 AN: 10608

Middle Eastern (MID) AF: 1.00 AC: 292 AN: 292

European-Non Finnish (NFE) AF: 0.999 AC: 67909 AN: 67950

Other (OTH) AF: 0.999 AC: 2113 AN: 2116

Alfa AF: 1.00 Hom.: 11806

Asia WGS AF: 1.00 AC: 3449 AN: 3450

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.0060
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs67769451; hg19: chr11-2930594;