chr11-63299431-T-C

Variant names:

• chr11-63299431-T-C
• rs515213
• NM_001039752.4:c.955-83T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001039752.4(SLC22A10):​c.955-83T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 1,099,846 control chromosomes in the GnomAD database, including 213,060 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.63 (30198 hom., cov: 31)
  • Exomes 𝑓: 0.62 (182862 hom.)
• Consequence: SLC22A10 NM_001039752.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 6 publications found

Genes affected

SLC22A10 (HGNC:18057): (solute carrier family 22 member 10) Predicted to enable transmembrane transporter activity. Predicted to be involved in organic anion transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039752.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A10	NM_001039752.4	MANE Select	c.955-83T>C		intron	N/A	NP_001034841.3
	SLC22A10	NR_134874.2		n.962-83T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A10	ENST00000332793.11	TSL:1 MANE Select	c.955-83T>C		intron	N/A	ENSP00000327569.6
	SLC22A10	ENST00000532724.5	TSL:1	n.498-83T>C		intron	N/A
	SLC22A10	ENST00000533483.5	TSL:1	n.799-83T>C		intron	N/A	ENSP00000433048.1

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95324 AN: 151836 Hom.: 30170 Cov.: 31

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.609

GnomAD4 exome AF: 0.617 AC: 585024 AN: 947892 Hom.: 182862 AF XY: 0.613 AC XY: 297578 AN XY: 485678

African (AFR) AF: 0.678 AC: 15891 AN: 23426

American (AMR) AF: 0.550 AC: 20254 AN: 36840

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 10027 AN: 21704

East Asian (EAS) AF: 0.412 AC: 14758 AN: 35834

South Asian (SAS) AF: 0.494 AC: 34522 AN: 69934

European-Finnish (FIN) AF: 0.640 AC: 32312 AN: 50452

Middle Eastern (MID) AF: 0.550 AC: 2639 AN: 4800

European-Non Finnish (NFE) AF: 0.647 AC: 428311 AN: 661846

Other (OTH) AF: 0.611 AC: 26310 AN: 43056

GnomAD4 genome AF: 0.628 AC: 95405 AN: 151954 Hom.: 30198 Cov.: 31 AF XY: 0.621 AC XY: 46152 AN XY: 74270

African (AFR) AF: 0.681 AC: 28219 AN: 41428

American (AMR) AF: 0.574 AC: 8752 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3472

East Asian (EAS) AF: 0.436 AC: 2249 AN: 5162

South Asian (SAS) AF: 0.488 AC: 2350 AN: 4818

European-Finnish (FIN) AF: 0.623 AC: 6578 AN: 10556

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43669 AN: 67960

Other (OTH) AF: 0.607 AC: 1278 AN: 2106

Alfa AF: 0.633 Hom.: 45041

Bravo AF: 0.629

Asia WGS AF: 0.518 AC: 1804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.48
PhyloP100		-0.49
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: rs515213; hg19: chr11-63066903; COSMIC: COSV60421666;