3-41096181-A-G

Position:

• chr3-41096181-A-G

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 0.595 in 151,958 control chromosomes in the GnomAD database, including 28,342 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 0.60 (28342 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 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: 0.595 AC: 90345 AN: 151840 Hom.: 28296 Cov.: 31

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.595 AC: 90449 AN: 151958 Hom.: 28342 Cov.: 31 AF XY: 0.586 AC XY: 43553 AN XY: 74272

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.578

Alfa AF: 0.543 Hom.: 27739

Bravo AF: 0.599

Asia WGS AF: 0.397 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs87938; hg19: chr3-41137672;