rs11242704

Variant names:

• chr6-1535763-A-G
• rs11242704
• ENST00000607350.2:n.129-6584T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-1535763-A-G
• chr6-1535763-A-T

Variant summary

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

The ENST00000607350.2(ENSG00000272279):​n.129-6584T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,848 control chromosomes in the GnomAD database, including 15,936 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 0.42 (15936 hom., cov: 30)
• Consequence: ENSG00000272279 ENST00000607350.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 12 publications found

Genes affected

ENSG00000272279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723944	XR_001743921.2	n.295-6608T>C		intron_variant	Intron 2 of 2
LOC102723944	XR_427861.4	n.234+16583T>C		intron_variant	Intron 2 of 6
LOC102723944	XR_926382.2	n.295-6584T>C		intron_variant	Intron 2 of 2
LOC102723944	XR_926384.2	n.260-6584T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272279	ENST00000607350.2	n.129-6584T>C		intron_variant	Intron 1 of 1	6
ENSG00000272279	ENST00000808963.1	n.224-6584T>C		intron_variant	Intron 2 of 2
ENSG00000272279	ENST00000808964.1	n.211-6608T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64301 AN: 151730 Hom.: 15907 Cov.: 30

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.392

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.424 AC: 64374 AN: 151848 Hom.: 15936 Cov.: 30 AF XY: 0.421 AC XY: 31248 AN XY: 74208

African (AFR) AF: 0.693 AC: 28662 AN: 41352

American (AMR) AF: 0.308 AC: 4697 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1028 AN: 3464

East Asian (EAS) AF: 0.475 AC: 2454 AN: 5164

South Asian (SAS) AF: 0.372 AC: 1790 AN: 4812

European-Finnish (FIN) AF: 0.314 AC: 3307 AN: 10526

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21144 AN: 67958

Other (OTH) AF: 0.389 AC: 819 AN: 2106

Alfa AF: 0.357 Hom.: 23933

Bravo AF: 0.436

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.68
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs11242704; hg19: chr6-1535998;