chr10-65894143-C-T

Variant names:

• chr10-65894143-C-T
• rs1942006

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 0.219 in 151,932 control chromosomes in the GnomAD database, including 4,423 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 0.22 (4423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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: 0.219 AC: 33301 AN: 151814 Hom.: 4426 Cov.: 32

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0679

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.219 AC: 33296 AN: 151932 Hom.: 4423 Cov.: 32 AF XY: 0.216 AC XY: 16051 AN XY: 74236

African (AFR) AF: 0.0821 AC: 3406 AN: 41486

American (AMR) AF: 0.273 AC: 4145 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3468

East Asian (EAS) AF: 0.0677 AC: 349 AN: 5156

South Asian (SAS) AF: 0.229 AC: 1100 AN: 4814

European-Finnish (FIN) AF: 0.208 AC: 2194 AN: 10558

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20127 AN: 67926

Other (OTH) AF: 0.245 AC: 518 AN: 2114

Alfa AF: 0.286 Hom.: 10177

Bravo AF: 0.216

Asia WGS AF: 0.136 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.0
DANN	Benign	0.29
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1942006; hg19: chr10-67653901;