4-64037888-T-C

Variant names:

• chr4-64037888-T-C
• rs28447044

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 0.341 in 151,938 control chromosomes in the GnomAD database, including 9,378 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 0.34 (9378 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 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: 0.341 AC: 51712 AN: 151820 Hom.: 9368 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.341 AC: 51758 AN: 151938 Hom.: 9378 Cov.: 31 AF XY: 0.343 AC XY: 25450 AN XY: 74278

African (AFR) AF: 0.232 AC: 9632 AN: 41456

American (AMR) AF: 0.427 AC: 6514 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3468

East Asian (EAS) AF: 0.181 AC: 933 AN: 5150

South Asian (SAS) AF: 0.477 AC: 2298 AN: 4814

European-Finnish (FIN) AF: 0.325 AC: 3427 AN: 10546

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26707 AN: 67936

Other (OTH) AF: 0.351 AC: 741 AN: 2110

Alfa AF: 0.232 Hom.: 535

Bravo AF: 0.340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.4
DANN	Benign	0.50
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs28447044; hg19: chr4-64903606;