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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.305

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11076397; hg19: chr16-60653220;