16-31101489-A-C

Variant names:

• chr16-31101489-A-C
• rs7187995

Variant summary

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

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 0.62 (27175 hom., cov: 17)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.64
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.624 AC: 83425 AN: 133710 Hom.: 27163 Cov.: 17

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.463

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.624 AC: 83459 AN: 133758 Hom.: 27175 Cov.: 17 AF XY: 0.620 AC XY: 39407 AN XY: 63534

African (AFR) AF: 0.706 AC: 24171 AN: 34228

American (AMR) AF: 0.587 AC: 7568 AN: 12900

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1668 AN: 3372

East Asian (EAS) AF: 0.100 AC: 490 AN: 4902

South Asian (SAS) AF: 0.816 AC: 3251 AN: 3982

European-Finnish (FIN) AF: 0.577 AC: 4103 AN: 7106

Middle Eastern (MID) AF: 0.453 AC: 125 AN: 276

European-Non Finnish (NFE) AF: 0.630 AC: 40536 AN: 64308

Other (OTH) AF: 0.581 AC: 1057 AN: 1820

Alfa AF: 0.471 Hom.: 957

Bravo AF: 0.622

Asia WGS AF: 0.524 AC: 1801 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.47
DANN	Benign	0.30
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs7187995; hg19: chr16-31112810;