3-122313942-G-A

Variant names:

• chr3-122313942-G-A
• rs2001548

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 0.124 in 152,116 control chromosomes in the GnomAD database, including 1,429 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 0.12 (1429 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.171 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: 0.124 AC: 18790 AN: 151998 Hom.: 1428 Cov.: 32

Gnomad AFR AF: 0.0520

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.124 AC: 18792 AN: 152116 Hom.: 1429 Cov.: 32 AF XY: 0.124 AC XY: 9207 AN XY: 74350

African (AFR) AF: 0.0521 AC: 2162 AN: 41510

American (AMR) AF: 0.144 AC: 2200 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3472

East Asian (EAS) AF: 0.0278 AC: 144 AN: 5178

South Asian (SAS) AF: 0.181 AC: 873 AN: 4818

European-Finnish (FIN) AF: 0.139 AC: 1475 AN: 10576

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10434 AN: 67978

Other (OTH) AF: 0.160 AC: 338 AN: 2106

Alfa AF: 0.140 Hom.: 405

Bravo AF: 0.120

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.0
DANN	Benign	0.24
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs2001548; hg19: chr3-122032789;