10-91900970-T-C

Variant names:

• chr10-91900970-T-C
• rs7919192

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 0.352 in 152,058 control chromosomes in the GnomAD database, including 10,007 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 0.35 (10007 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 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: 0.352 AC: 53470 AN: 151940 Hom.: 9993 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.352 AC: 53518 AN: 152058 Hom.: 10007 Cov.: 32 AF XY: 0.345 AC XY: 25688 AN XY: 74356

African (AFR) AF: 0.469 AC: 19451 AN: 41470

American (AMR) AF: 0.277 AC: 4231 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3472

East Asian (EAS) AF: 0.181 AC: 937 AN: 5172

South Asian (SAS) AF: 0.198 AC: 950 AN: 4806

European-Finnish (FIN) AF: 0.259 AC: 2743 AN: 10580

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22937 AN: 67962

Other (OTH) AF: 0.352 AC: 743 AN: 2110

Alfa AF: 0.341 Hom.: 14834

Bravo AF: 0.359

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.21
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7919192; hg19: chr10-93660727;