rs35509282

Variant names:

• chr4-162412253-T-A
• rs35509282

Your query was ambiguous. Multiple possible variants found:

• chr4-162412253-T-A
• chr4-162412253-T-C
• chr4-162412253-T-G

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 0.154 in 151,866 control chromosomes in the GnomAD database, including 2,194 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 0.15 (2194 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 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: 0.154 AC: 23411 AN: 151748 Hom.: 2185 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.154 AC: 23442 AN: 151866 Hom.: 2194 Cov.: 32 AF XY: 0.161 AC XY: 11969 AN XY: 74206

African (AFR) AF: 0.171 AC: 7066 AN: 41416

American (AMR) AF: 0.217 AC: 3303 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3472

East Asian (EAS) AF: 0.419 AC: 2141 AN: 5114

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4808

European-Finnish (FIN) AF: 0.166 AC: 1747 AN: 10554

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7471 AN: 67954

Other (OTH) AF: 0.144 AC: 303 AN: 2100

Alfa AF: 0.135 Hom.: 193

Bravo AF: 0.157

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.3
DANN	Benign	0.56
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs35509282; hg19: chr4-163333405;