rs4739071

Variant names:

• chr8-63258564-A-C
• rs4739071

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 0.15 in 152,124 control chromosomes in the GnomAD database, including 2,200 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 0.15 (2200 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 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: 0.150 AC: 22851 AN: 152006 Hom.: 2191 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.0843

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.150 AC: 22890 AN: 152124 Hom.: 2200 Cov.: 32 AF XY: 0.150 AC XY: 11175 AN XY: 74392

African (AFR) AF: 0.265 AC: 10980 AN: 41492

American (AMR) AF: 0.155 AC: 2373 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1488 AN: 5160

South Asian (SAS) AF: 0.107 AC: 516 AN: 4822

European-Finnish (FIN) AF: 0.100 AC: 1062 AN: 10594

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.0844 AC: 5735 AN: 67990

Other (OTH) AF: 0.144 AC: 304 AN: 2110

Alfa AF: 0.103 Hom.: 589

Bravo AF: 0.159

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.36
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs4739071; hg19: chr8-64171122;