3-172441415-G-A

Variant names:

• chr3-172441415-G-A
• rs4144707

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 0.639 in 152,008 control chromosomes in the GnomAD database, including 31,796 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 0.64 (31796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97060 AN: 151892 Hom.: 31789 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.639 AC: 97107 AN: 152008 Hom.: 31796 Cov.: 32 AF XY: 0.635 AC XY: 47180 AN XY: 74284

African (AFR) AF: 0.494 AC: 20482 AN: 41436

American (AMR) AF: 0.691 AC: 10558 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2285 AN: 3470

East Asian (EAS) AF: 0.640 AC: 3308 AN: 5170

South Asian (SAS) AF: 0.459 AC: 2208 AN: 4812

European-Finnish (FIN) AF: 0.689 AC: 7288 AN: 10570

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.717 AC: 48748 AN: 67960

Other (OTH) AF: 0.664 AC: 1403 AN: 2112

Alfa AF: 0.646 Hom.: 4967

Bravo AF: 0.640

Asia WGS AF: 0.534 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.30
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs4144707; hg19: chr3-172159205;