10-53623595-A-T

Variant names:

• chr10-53623595-A-T
• rs17345

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 0.19 in 151,948 control chromosomes in the GnomAD database, including 3,463 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 (3463 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• 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 (AFR) allele frequency at 95% confidence interval = 0.328 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: 0.190 AC: 28866 AN: 151830 Hom.: 3463 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.190 AC: 28890 AN: 151948 Hom.: 3463 Cov.: 31 AF XY: 0.188 AC XY: 13964 AN XY: 74282

African (AFR) AF: 0.333 AC: 13768 AN: 41352

American (AMR) AF: 0.154 AC: 2355 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3468

East Asian (EAS) AF: 0.0440 AC: 228 AN: 5176

South Asian (SAS) AF: 0.0837 AC: 403 AN: 4814

European-Finnish (FIN) AF: 0.160 AC: 1696 AN: 10568

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9334 AN: 67976

Other (OTH) AF: 0.194 AC: 410 AN: 2108

Alfa AF: 0.170 Hom.: 327

Bravo AF: 0.194

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.74
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs17345; hg19: chr10-55383355;