3-41043968-G-A

Variant names:

• chr3-41043968-G-A
• rs106871

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 0.352 in 151,752 control chromosomes in the GnomAD database, including 10,912 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 0.35 (10912 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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: 0.352 AC: 53400 AN: 151632 Hom.: 10904 Cov.: 30

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.352 AC: 53421 AN: 151752 Hom.: 10912 Cov.: 30 AF XY: 0.350 AC XY: 25981 AN XY: 74142

African (AFR) AF: 0.142 AC: 5854 AN: 41358

American (AMR) AF: 0.408 AC: 6238 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1177 AN: 3466

East Asian (EAS) AF: 0.352 AC: 1804 AN: 5118

South Asian (SAS) AF: 0.289 AC: 1388 AN: 4804

European-Finnish (FIN) AF: 0.442 AC: 4649 AN: 10514

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31062 AN: 67894

Other (OTH) AF: 0.372 AC: 786 AN: 2114

Alfa AF: 0.424 Hom.: 62082

Bravo AF: 0.344

Asia WGS AF: 0.313 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.60
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs106871; hg19: chr3-41085459; COSMIC: COSV66488192;