4-63016944-T-G

Variant names:

• chr4-63016944-T-G
• rs2346645

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 0.911 in 152,140 control chromosomes in the GnomAD database, including 63,899 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 0.91 (63899 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 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: 0.911 AC: 138530 AN: 152022 Hom.: 63855 Cov.: 33

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.911 AC: 138628 AN: 152140 Hom.: 63899 Cov.: 33 AF XY: 0.907 AC XY: 67434 AN XY: 74366

African (AFR) AF: 0.804 AC: 33336 AN: 41466

American (AMR) AF: 0.900 AC: 13755 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.994 AC: 3451 AN: 3472

East Asian (EAS) AF: 0.625 AC: 3222 AN: 5158

South Asian (SAS) AF: 0.867 AC: 4185 AN: 4826

European-Finnish (FIN) AF: 0.981 AC: 10406 AN: 10612

Middle Eastern (MID) AF: 0.976 AC: 285 AN: 292

European-Non Finnish (NFE) AF: 0.987 AC: 67136 AN: 68004

Other (OTH) AF: 0.917 AC: 1941 AN: 2116

Alfa AF: 0.943 Hom.: 4133

Bravo AF: 0.902

Asia WGS AF: 0.767 AC: 2662 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.069
DANN	Benign	0.56
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2346645; hg19: chr4-63882662;