rs4812744

Variant names:

• chr20-43856709-T-C
• rs4812744

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 0.758 in 152,142 control chromosomes in the GnomAD database, including 44,175 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 0.76 (44175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.776 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: 0.758 AC: 115285 AN: 152024 Hom.: 44145 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.758 AC: 115356 AN: 152142 Hom.: 44175 Cov.: 32 AF XY: 0.751 AC XY: 55866 AN XY: 74376

African (AFR) AF: 0.779 AC: 32297 AN: 41484

American (AMR) AF: 0.707 AC: 10807 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2750 AN: 3472

East Asian (EAS) AF: 0.478 AC: 2475 AN: 5180

South Asian (SAS) AF: 0.553 AC: 2667 AN: 4820

European-Finnish (FIN) AF: 0.821 AC: 8679 AN: 10576

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53145 AN: 68000

Other (OTH) AF: 0.741 AC: 1565 AN: 2112

Alfa AF: 0.766 Hom.: 67536

Bravo AF: 0.752

Asia WGS AF: 0.557 AC: 1936 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.82
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs4812744; hg19: chr20-42485349;