rs4385797

Variant names:

• chr10-52861270-G-A
• rs4385797

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 0.279 in 152,018 control chromosomes in the GnomAD database, including 6,505 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 0.28 (6505 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 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: 0.279 AC: 42449 AN: 151900 Hom.: 6503 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.279 AC: 42465 AN: 152018 Hom.: 6505 Cov.: 33 AF XY: 0.279 AC XY: 20712 AN XY: 74312

African (AFR) AF: 0.147 AC: 6093 AN: 41478

American (AMR) AF: 0.322 AC: 4918 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1852 AN: 5162

South Asian (SAS) AF: 0.308 AC: 1486 AN: 4822

European-Finnish (FIN) AF: 0.312 AC: 3295 AN: 10558

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.335 AC: 22773 AN: 67938

Other (OTH) AF: 0.298 AC: 629 AN: 2114

Alfa AF: 0.291 Hom.: 1087

Bravo AF: 0.273

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4385797; hg19: chr10-54621030;