8-20041535-C-T

Variant names:

• chr8-20041535-C-T
• rs4244457

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 0.722 in 151,988 control chromosomes in the GnomAD database, including 41,113 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 0.72 (41113 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 18 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 (AFR) allele frequency at 95% confidence interval = 0.9 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: 0.722 AC: 109698 AN: 151870 Hom.: 41059 Cov.: 30

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.722 AC: 109793 AN: 151988 Hom.: 41113 Cov.: 30 AF XY: 0.715 AC XY: 53132 AN XY: 74290

African (AFR) AF: 0.908 AC: 37669 AN: 41482

American (AMR) AF: 0.625 AC: 9530 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2669 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1694 AN: 5138

South Asian (SAS) AF: 0.521 AC: 2510 AN: 4818

European-Finnish (FIN) AF: 0.676 AC: 7134 AN: 10560

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46181 AN: 67950

Other (OTH) AF: 0.699 AC: 1475 AN: 2110

Alfa AF: 0.688 Hom.: 141427

Bravo AF: 0.724

Asia WGS AF: 0.458 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.39
DANN	Benign	0.50
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs4244457; hg19: chr8-19899046;