rs11715496

Variant names:

• chr3-48595812-C-A
• rs11715496

Your query was ambiguous. Multiple possible variants found:

• chr3-48595812-C-A
• chr3-48595812-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0159 in 152,298 control chromosomes in the GnomAD database, including 40 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 0.016 (40 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0159 (2429/152298) while in subpopulation SAS AF = 0.041 (198/4824). AF 95% confidence interval is 0.0364. There are 40 homozygotes in GnomAd4. There are 1169 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 40 gene

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: 0.0160 AC: 2428 AN: 152180 Hom.: 41 Cov.: 32

Gnomad AFR AF: 0.00454

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0103

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.00367

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0159 AC: 2429 AN: 152298 Hom.: 40 Cov.: 32 AF XY: 0.0157 AC XY: 1169 AN XY: 74476

African (AFR) AF: 0.00452 AC: 188 AN: 41568

American (AMR) AF: 0.0103 AC: 158 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0772 AC: 268 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0410 AC: 198 AN: 4824

European-Finnish (FIN) AF: 0.00367 AC: 39 AN: 10628

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0222 AC: 1509 AN: 68004

Other (OTH) AF: 0.0189 AC: 40 AN: 2112

Alfa AF: 0.0207 Hom.: 64

Bravo AF: 0.0154

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.8
DANN	Benign	0.46
PhyloP100		-0.13
PromoterAI		-0.063	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11715496; hg19: chr3-48633245;