chr5-35881341-G-A

Variant names:

• chr5-35881341-G-A
• rs11742270

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 0.2 in 152,062 control chromosomes in the GnomAD database, including 3,731 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 0.20 (3731 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 16 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 = 0.262 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: 0.200 AC: 30398 AN: 151944 Hom.: 3733 Cov.: 32

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.200 AC: 30399 AN: 152062 Hom.: 3731 Cov.: 32 AF XY: 0.202 AC XY: 15043 AN XY: 74336

African (AFR) AF: 0.0652 AC: 2704 AN: 41486

American (AMR) AF: 0.174 AC: 2668 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3464

East Asian (EAS) AF: 0.165 AC: 851 AN: 5168

South Asian (SAS) AF: 0.201 AC: 966 AN: 4808

European-Finnish (FIN) AF: 0.346 AC: 3653 AN: 10564

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18039 AN: 67964

Other (OTH) AF: 0.184 AC: 388 AN: 2110

Alfa AF: 0.246 Hom.: 2109

Bravo AF: 0.182

Asia WGS AF: 0.204 AC: 710 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	9.5
DANN	Benign	0.73
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs11742270; hg19: chr5-35881443;