chr5-3581646-G-A

Variant names:

• chr5-3581646-G-A
• rs10042985

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 0.414 in 152,034 control chromosomes in the GnomAD database, including 14,269 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 0.41 (14269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 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: 0.414 AC: 62957 AN: 151914 Hom.: 14273 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.414 AC: 62962 AN: 152034 Hom.: 14269 Cov.: 32 AF XY: 0.419 AC XY: 31103 AN XY: 74310

African (AFR) AF: 0.227 AC: 9412 AN: 41480

American (AMR) AF: 0.461 AC: 7036 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1615 AN: 3466

East Asian (EAS) AF: 0.454 AC: 2345 AN: 5162

South Asian (SAS) AF: 0.366 AC: 1767 AN: 4824

European-Finnish (FIN) AF: 0.539 AC: 5690 AN: 10558

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33468 AN: 67956

Other (OTH) AF: 0.446 AC: 943 AN: 2112

Alfa AF: 0.470 Hom.: 78295

Bravo AF: 0.402

Asia WGS AF: 0.353 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.70
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10042985; hg19: chr5-3581760;