rs11763963

Positions:

• chr7-26605814-T-C
• chr7-26605814-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661238.1(ENSG00000286507):​n.49-2297A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0575 in 152,172 control chromosomes in the GnomAD database, including 406 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 0.058 (406 hom., cov: 32)
• Consequence: ENST00000661238.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928077	XR_007060264.1	n.1167-6444A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661238.1	n.49-2297A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0576 AC: 8756 AN: 152054 Hom.: 407 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.0825

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.0609

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

GnomAD4 genome AF: 0.0575 AC: 8751 AN: 152172 Hom.: 406 Cov.: 32 AF XY: 0.0589 AC XY: 4381 AN XY: 74388

Gnomad4 AFR AF: 0.0168

Gnomad4 AMR AF: 0.0485

Gnomad4 ASJ AF: 0.0825

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.0861

Gnomad4 FIN AF: 0.0839

Gnomad4 NFE AF: 0.0617

Gnomad4 OTH AF: 0.0593

Alfa AF: 0.0558 Hom.: 33

Bravo AF: 0.0536

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11763963; hg19: chr7-26645433;