rs11076397

Variant names:

• chr16-60619316-T-A
• rs11076397

Your query was ambiguous. Multiple possible variants found:

• chr16-60619316-T-A
• chr16-60619316-T-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.284 in 151,716 control chromosomes in the GnomAD database, including 6,967 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 0.28 (6967 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.17
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 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: 0.284 AC: 43119 AN: 151598 Hom.: 6955 Cov.: 31

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.284 AC: 43140 AN: 151716 Hom.: 6967 Cov.: 31 AF XY: 0.290 AC XY: 21468 AN XY: 74118

African (AFR) AF: 0.118 AC: 4892 AN: 41416

American (AMR) AF: 0.345 AC: 5249 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3466

East Asian (EAS) AF: 0.460 AC: 2367 AN: 5144

South Asian (SAS) AF: 0.405 AC: 1949 AN: 4816

European-Finnish (FIN) AF: 0.346 AC: 3615 AN: 10448

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.338 AC: 22966 AN: 67918

Other (OTH) AF: 0.305 AC: 640 AN: 2100

Alfa AF: 0.291 Hom.: 848

Bravo AF: 0.279

Asia WGS AF: 0.394 AC: 1373 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	20
DANN	Benign	0.66
PhyloP100		3.2

Splicing

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

Other links and lift over

dbSNP: rs11076397; hg19: chr16-60653220;