chr10-83867491-G-T

Variant names:

• chr10-83867491-G-T
• rs7901651

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 0.404 in 152,042 control chromosomes in the GnomAD database, including 12,584 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 0.40 (12584 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 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: 0.404 AC: 61403 AN: 151922 Hom.: 12558 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.404 AC: 61479 AN: 152042 Hom.: 12584 Cov.: 32 AF XY: 0.401 AC XY: 29820 AN XY: 74316

African (AFR) AF: 0.387 AC: 16040 AN: 41484

American (AMR) AF: 0.438 AC: 6694 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1532 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1716 AN: 5168

South Asian (SAS) AF: 0.353 AC: 1700 AN: 4820

European-Finnish (FIN) AF: 0.315 AC: 3325 AN: 10552

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28949 AN: 67960

Other (OTH) AF: 0.440 AC: 929 AN: 2110

Alfa AF: 0.412 Hom.: 2301

Bravo AF: 0.416

Asia WGS AF: 0.323 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.6
DANN	Benign	0.63
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs7901651; hg19: chr10-85627247;