rs934498

Variant names:

• chr4-4260279-G-T
• rs934498

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 0.317 in 151,988 control chromosomes in the GnomAD database, including 8,347 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 0.32 (8347 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 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: 0.317 AC: 48164 AN: 151868 Hom.: 8319 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.317 AC: 48242 AN: 151988 Hom.: 8347 Cov.: 32 AF XY: 0.324 AC XY: 24103 AN XY: 74282

African (AFR) AF: 0.428 AC: 17741 AN: 41420

American (AMR) AF: 0.409 AC: 6246 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3464

East Asian (EAS) AF: 0.286 AC: 1478 AN: 5172

South Asian (SAS) AF: 0.491 AC: 2363 AN: 4808

European-Finnish (FIN) AF: 0.226 AC: 2394 AN: 10576

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16371 AN: 67960

Other (OTH) AF: 0.298 AC: 629 AN: 2110

Alfa AF: 0.278 Hom.: 1041

Bravo AF: 0.332

Asia WGS AF: 0.383 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.47
DANN	Benign	0.35
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs934498; hg19: chr4-4262006;