rs1303615

Variant names:

• chr11-60117647-C-T
• rs1303615

Variant summary

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

The variant allele was found at a frequency of 0.437 in 152,008 control chromosomes in the GnomAD database, including 14,790 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 0.44 (14790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 12 publications found

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 (SAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66408 AN: 151890 Hom.: 14767 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.437 AC: 66475 AN: 152008 Hom.: 14790 Cov.: 32 AF XY: 0.431 AC XY: 32067 AN XY: 74316

African (AFR) AF: 0.482 AC: 19976 AN: 41458

American (AMR) AF: 0.358 AC: 5461 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1606 AN: 3466

East Asian (EAS) AF: 0.375 AC: 1944 AN: 5188

South Asian (SAS) AF: 0.547 AC: 2641 AN: 4828

European-Finnish (FIN) AF: 0.308 AC: 3251 AN: 10564

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30062 AN: 67928

Other (OTH) AF: 0.465 AC: 981 AN: 2110

Alfa AF: 0.420 Hom.: 2208

Bravo AF: 0.439

Asia WGS AF: 0.461 AC: 1604 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.72
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1303615; hg19: chr11-59885120;