rs35964658

Variant names:

• chr4-141758435-A-G
• rs35964658

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 0.0927 in 152,198 control chromosomes in the GnomAD database, including 1,275 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 0.093 (1275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 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: 0.0926 AC: 14089 AN: 152080 Hom.: 1271 Cov.: 32

Gnomad AFR AF: 0.0347

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0726

Gnomad OTH AF: 0.0867

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

GnomAD4 genome AF: 0.0927 AC: 14105 AN: 152198 Hom.: 1275 Cov.: 32 AF XY: 0.0987 AC XY: 7344 AN XY: 74376

African (AFR) AF: 0.0349 AC: 1449 AN: 41544

American (AMR) AF: 0.237 AC: 3619 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3472

East Asian (EAS) AF: 0.427 AC: 2209 AN: 5170

South Asian (SAS) AF: 0.110 AC: 529 AN: 4814

European-Finnish (FIN) AF: 0.0925 AC: 980 AN: 10598

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0726 AC: 4936 AN: 68008

Other (OTH) AF: 0.0886 AC: 187 AN: 2110

Alfa AF: 0.100 Hom.: 270

Bravo AF: 0.105

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.6
DANN	Benign	0.82
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs35964658; hg19: chr4-142679588;