chr16-9128037-G-C

Variant names:

• chr16-9128037-G-C
• rs2313980

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 0.671 in 151,802 control chromosomes in the GnomAD database, including 35,587 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 0.67 (35587 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 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: 0.671 AC: 101805 AN: 151684 Hom.: 35519 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.671 AC: 101932 AN: 151802 Hom.: 35587 Cov.: 31 AF XY: 0.669 AC XY: 49635 AN XY: 74186

African (AFR) AF: 0.871 AC: 36070 AN: 41422

American (AMR) AF: 0.645 AC: 9846 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2069 AN: 3466

East Asian (EAS) AF: 0.463 AC: 2380 AN: 5144

South Asian (SAS) AF: 0.498 AC: 2396 AN: 4808

European-Finnish (FIN) AF: 0.643 AC: 6769 AN: 10528

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.594 AC: 40292 AN: 67868

Other (OTH) AF: 0.625 AC: 1316 AN: 2106

Alfa AF: 0.521 Hom.: 1465

Bravo AF: 0.679

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.44
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2313980; hg19: chr16-9221894;