rs10816481

Variant names:

• chr9-107280203-T-C
• rs10816481

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 0.634 in 152,138 control chromosomes in the GnomAD database, including 31,709 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 0.63 (31709 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.71 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: 0.634 AC: 96379 AN: 152020 Hom.: 31690 Cov.: 34

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.634 AC: 96434 AN: 152138 Hom.: 31709 Cov.: 34 AF XY: 0.633 AC XY: 47075 AN XY: 74376

African (AFR) AF: 0.478 AC: 19807 AN: 41474

American (AMR) AF: 0.701 AC: 10720 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2449 AN: 3472

East Asian (EAS) AF: 0.354 AC: 1829 AN: 5162

South Asian (SAS) AF: 0.499 AC: 2406 AN: 4824

European-Finnish (FIN) AF: 0.790 AC: 8376 AN: 10604

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48653 AN: 67998

Other (OTH) AF: 0.621 AC: 1311 AN: 2110

Alfa AF: 0.690 Hom.: 58104

Bravo AF: 0.624

Asia WGS AF: 0.436 AC: 1518 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	0.77
DANN	Benign	0.41
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs10816481; hg19: chr9-110042484;