rs934498

chr4-4260279-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.298

Alfa AF: 0.272 Hom.: 965

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs934498; hg19: chr4-4262006;