10-56579481-T-C

Variant names:

• chr10-56579481-T-C
• rs1907926

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 0.185 in 151,956 control chromosomes in the GnomAD database, including 3,320 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 0.19 (3320 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 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: 0.185 AC: 28109 AN: 151838 Hom.: 3310 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.185 AC: 28158 AN: 151956 Hom.: 3320 Cov.: 32 AF XY: 0.184 AC XY: 13704 AN XY: 74286

African (AFR) AF: 0.333 AC: 13807 AN: 41418

American (AMR) AF: 0.209 AC: 3177 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3468

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5178

South Asian (SAS) AF: 0.103 AC: 499 AN: 4826

European-Finnish (FIN) AF: 0.161 AC: 1701 AN: 10584

Middle Eastern (MID) AF: 0.169 AC: 49 AN: 290

European-Non Finnish (NFE) AF: 0.118 AC: 8018 AN: 67950

Other (OTH) AF: 0.164 AC: 346 AN: 2104

Alfa AF: 0.120 Hom.: 922

Bravo AF: 0.199

Asia WGS AF: 0.0740 AC: 256 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.1
DANN	Benign	0.72
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs1907926; hg19: chr10-58339241;