rs842873

Variant names:

• chr4-71830748-C-G
• rs842873

Your query was ambiguous. Multiple possible variants found:

• chr4-71830748-C-G
• chr4-71830748-C-T

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 0.59 in 152,036 control chromosomes in the GnomAD database, including 28,571 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 0.59 (28571 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.828 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: 0.590 AC: 89610 AN: 151920 Hom.: 28518 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.590 AC: 89719 AN: 152036 Hom.: 28571 Cov.: 32 AF XY: 0.586 AC XY: 43578 AN XY: 74310

African (AFR) AF: 0.836 AC: 34683 AN: 41502

American (AMR) AF: 0.500 AC: 7632 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1521 AN: 3470

East Asian (EAS) AF: 0.841 AC: 4350 AN: 5174

South Asian (SAS) AF: 0.461 AC: 2223 AN: 4818

European-Finnish (FIN) AF: 0.458 AC: 4834 AN: 10548

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32602 AN: 67938

Other (OTH) AF: 0.565 AC: 1194 AN: 2114

Alfa AF: 0.535 Hom.: 2670

Bravo AF: 0.610

Asia WGS AF: 0.638 AC: 2222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs842873; hg19: chr4-72696465;