chr10-55789536-C-T

Variant names:

• chr10-55789536-C-T
• rs16907840

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 0.176 in 150,446 control chromosomes in the GnomAD database, including 2,542 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 0.18 (2542 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.204 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: 0.176 AC: 26468 AN: 150336 Hom.: 2536 Cov.: 30

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.0651

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.176 AC: 26488 AN: 150446 Hom.: 2542 Cov.: 30 AF XY: 0.169 AC XY: 12427 AN XY: 73468

African (AFR) AF: 0.162 AC: 6672 AN: 41172

American (AMR) AF: 0.171 AC: 2555 AN: 14950

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3462

East Asian (EAS) AF: 0.00118 AC: 6 AN: 5106

South Asian (SAS) AF: 0.0659 AC: 316 AN: 4798

European-Finnish (FIN) AF: 0.152 AC: 1563 AN: 10278

Middle Eastern (MID) AF: 0.241 AC: 70 AN: 290

European-Non Finnish (NFE) AF: 0.207 AC: 13942 AN: 67394

Other (OTH) AF: 0.205 AC: 428 AN: 2086

Alfa AF: 0.200 Hom.: 4625

Bravo AF: 0.179

Asia WGS AF: 0.0410 AC: 142 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	2.5
DANN	Benign	0.39
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs16907840; hg19: chr10-57549296;