rs4934256

Variant names:

• chr10-86740608-A-G
• rs4934256

Your query was ambiguous. Multiple possible variants found:

• chr10-86740608-A-G
• chr10-86740608-A-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 0.0554 in 151,710 control chromosomes in the GnomAD database, including 345 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 0.055 (345 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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 (NFE) allele frequency at 95% confidence interval = 0.0711 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: 0.0555 AC: 8409 AN: 151592 Hom.: 345 Cov.: 29

Gnomad AFR AF: 0.0180

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0419

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.0232

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0728

Gnomad OTH AF: 0.0594

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

GnomAD4 genome AF: 0.0554 AC: 8410 AN: 151710 Hom.: 345 Cov.: 29 AF XY: 0.0570 AC XY: 4228 AN XY: 74124

Gnomad4 AFR AF: 0.0181

Gnomad4 AMR AF: 0.0418

Gnomad4 ASJ AF: 0.0280

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.0318

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.0728

Gnomad4 OTH AF: 0.0588

Alfa AF: 0.0600 Hom.: 43

Bravo AF: 0.0477

Asia WGS AF: 0.0450 AC: 158 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	0.30
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4934256; hg19: chr10-88500365;