3-108229404-G-C

Variant names:

• chr3-108229404-G-C
• rs1289742

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 0.86 in 152,252 control chromosomes in the GnomAD database, including 57,218 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 0.86 (57218 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.938 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: 0.860 AC: 130862 AN: 152134 Hom.: 57198 Cov.: 33

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.860 AC: 130928 AN: 152252 Hom.: 57218 Cov.: 33 AF XY: 0.852 AC XY: 63450 AN XY: 74436

African (AFR) AF: 0.779 AC: 32337 AN: 41520

American (AMR) AF: 0.801 AC: 12248 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3341 AN: 3472

East Asian (EAS) AF: 0.482 AC: 2492 AN: 5172

South Asian (SAS) AF: 0.807 AC: 3897 AN: 4830

European-Finnish (FIN) AF: 0.880 AC: 9332 AN: 10604

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.944 AC: 64257 AN: 68036

Other (OTH) AF: 0.876 AC: 1850 AN: 2112

Alfa AF: 0.892 Hom.: 3012

Bravo AF: 0.850

Asia WGS AF: 0.637 AC: 2217 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	11
DANN	Benign	0.48
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs1289742; hg19: chr3-107948251;