rs521674

Variant names:

• chr10-111075832-T-A
• rs521674

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 0.568 in 152,080 control chromosomes in the GnomAD database, including 28,320 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 0.57 (28320 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.731 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: 0.568 AC: 86329 AN: 151962 Hom.: 28333 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.568 AC: 86325 AN: 152080 Hom.: 28320 Cov.: 32 AF XY: 0.567 AC XY: 42150 AN XY: 74330

African (AFR) AF: 0.246 AC: 10203 AN: 41462

American (AMR) AF: 0.612 AC: 9362 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2495 AN: 3466

East Asian (EAS) AF: 0.328 AC: 1694 AN: 5168

South Asian (SAS) AF: 0.461 AC: 2219 AN: 4812

European-Finnish (FIN) AF: 0.775 AC: 8201 AN: 10578

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 50048 AN: 67988

Other (OTH) AF: 0.582 AC: 1226 AN: 2106

Alfa AF: 0.691 Hom.: 20889

Bravo AF: 0.543

Asia WGS AF: 0.361 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	10
DANN	Benign	0.79
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs521674; hg19: chr10-112835590;