rs10941679

Variant names:

• chr5-44706396-A-G
• rs10941679

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 0.254 in 151,982 control chromosomes in the GnomAD database, including 5,365 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 0.25 (5365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 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: 0.254 AC: 38550 AN: 151864 Hom.: 5344 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.254 AC: 38596 AN: 151982 Hom.: 5365 Cov.: 32 AF XY: 0.260 AC XY: 19313 AN XY: 74278

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.267

Alfa AF: 0.257 Hom.: 2386

Bravo AF: 0.257

Asia WGS AF: 0.431 AC: 1497 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10941679; hg19: chr5-44706498;