chr4-64046483-G-A

Variant names:

• chr4-64046483-G-A
• rs2053844

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 0.388 in 151,754 control chromosomes in the GnomAD database, including 11,723 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 0.39 (11723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 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: 0.388 AC: 58867 AN: 151636 Hom.: 11702 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.388 AC: 58944 AN: 151754 Hom.: 11723 Cov.: 32 AF XY: 0.388 AC XY: 28790 AN XY: 74154

African (AFR) AF: 0.400 AC: 16559 AN: 41410

American (AMR) AF: 0.444 AC: 6750 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3468

East Asian (EAS) AF: 0.162 AC: 833 AN: 5150

South Asian (SAS) AF: 0.475 AC: 2290 AN: 4816

European-Finnish (FIN) AF: 0.327 AC: 3445 AN: 10540

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.394 AC: 26731 AN: 67848

Other (OTH) AF: 0.391 AC: 822 AN: 2102

Alfa AF: 0.394 Hom.: 4387

Bravo AF: 0.393

Asia WGS AF: 0.382 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.17
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2053844; hg19: chr4-64912201;