3-122641075-A-T

Variant names:

• chr3-122641075-A-T
• rs1256196

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 0.367 in 151,936 control chromosomes in the GnomAD database, including 12,008 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 0.37 (12008 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55712 AN: 151818 Hom.: 11958 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.367 AC: 55832 AN: 151936 Hom.: 12008 Cov.: 32 AF XY: 0.361 AC XY: 26804 AN XY: 74232

African (AFR) AF: 0.600 AC: 24839 AN: 41428

American (AMR) AF: 0.267 AC: 4071 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3466

East Asian (EAS) AF: 0.0424 AC: 220 AN: 5186

South Asian (SAS) AF: 0.244 AC: 1178 AN: 4822

European-Finnish (FIN) AF: 0.323 AC: 3394 AN: 10524

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20102 AN: 67934

Other (OTH) AF: 0.349 AC: 737 AN: 2112

Alfa AF: 0.220 Hom.: 530

Bravo AF: 0.374

Asia WGS AF: 0.221 AC: 770 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.63
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs1256196; hg19: chr3-122359922; COSMIC: COSV59971931;