chr3-42291132-T-G

Variant names:

• chr3-42291132-T-G
• rs9839267

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 0.153 in 152,146 control chromosomes in the GnomAD database, including 2,187 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 0.15 (2187 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 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: 0.152 AC: 23157 AN: 152026 Hom.: 2177 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.153 AC: 23204 AN: 152146 Hom.: 2187 Cov.: 32 AF XY: 0.150 AC XY: 11188 AN XY: 74390

African (AFR) AF: 0.259 AC: 10725 AN: 41484

American (AMR) AF: 0.144 AC: 2195 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0591 AC: 205 AN: 3466

East Asian (EAS) AF: 0.149 AC: 767 AN: 5162

South Asian (SAS) AF: 0.154 AC: 745 AN: 4822

European-Finnish (FIN) AF: 0.0767 AC: 813 AN: 10604

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7374 AN: 68008

Other (OTH) AF: 0.134 AC: 282 AN: 2112

Alfa AF: 0.0940 Hom.: 252

Bravo AF: 0.164

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.55
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs9839267; hg19: chr3-42332624;