rs16960741

Variant names:

• chr16-12814452-G-A
• rs16960741

Your query was ambiguous. Multiple possible variants found:

• chr16-12814452-G-A
• chr16-12814452-G-C

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 0.112 in 152,060 control chromosomes in the GnomAD database, including 1,808 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 0.11 (1808 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17028 AN: 151940 Hom.: 1798 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.0693

Gnomad FIN AF: 0.0176

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0293

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.112 AC: 17080 AN: 152060 Hom.: 1808 Cov.: 32 AF XY: 0.112 AC XY: 8295 AN XY: 74336

African (AFR) AF: 0.261 AC: 10805 AN: 41458

American (AMR) AF: 0.125 AC: 1903 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0640 AC: 222 AN: 3468

East Asian (EAS) AF: 0.257 AC: 1328 AN: 5158

South Asian (SAS) AF: 0.0691 AC: 333 AN: 4818

European-Finnish (FIN) AF: 0.0176 AC: 186 AN: 10586

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0293 AC: 1992 AN: 67988

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.0551 Hom.: 2370

Bravo AF: 0.126

Asia WGS AF: 0.194 AC: 676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.65
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs16960741; hg19: chr16-12908309;