10-57660887-T-C

Variant names:

• chr10-57660887-T-C
• rs4428995

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 0.635 in 152,152 control chromosomes in the GnomAD database, including 31,279 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 0.64 (31279 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.636 AC: 96638 AN: 152034 Hom.: 31291 Cov.: 33

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.635 AC: 96668 AN: 152152 Hom.: 31279 Cov.: 33 AF XY: 0.631 AC XY: 46897 AN XY: 74378

African (AFR) AF: 0.545 AC: 22604 AN: 41504

American (AMR) AF: 0.558 AC: 8527 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2490 AN: 3470

East Asian (EAS) AF: 0.759 AC: 3920 AN: 5166

South Asian (SAS) AF: 0.500 AC: 2409 AN: 4820

European-Finnish (FIN) AF: 0.668 AC: 7067 AN: 10578

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47414 AN: 68010

Other (OTH) AF: 0.653 AC: 1380 AN: 2114

Alfa AF: 0.679 Hom.: 55179

Bravo AF: 0.628

Asia WGS AF: 0.595 AC: 2071 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.3
DANN	Benign	0.77
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs4428995; hg19: chr10-59420647;