rs4710189

Variant names:

• chr6-167142836-G-A
• rs4710189

Your query was ambiguous. Multiple possible variants found:

• chr6-167142836-G-A
• chr6-167142836-G-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 0.708 in 152,206 control chromosomes in the GnomAD database, including 38,475 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 0.71 (38475 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 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: 0.708 AC: 107665 AN: 152088 Hom.: 38433 Cov.: 33

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.708 AC: 107768 AN: 152206 Hom.: 38475 Cov.: 33 AF XY: 0.705 AC XY: 52487 AN XY: 74418

African (AFR) AF: 0.792 AC: 32888 AN: 41536

American (AMR) AF: 0.783 AC: 11963 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2378 AN: 3472

East Asian (EAS) AF: 0.595 AC: 3082 AN: 5178

South Asian (SAS) AF: 0.678 AC: 3265 AN: 4816

European-Finnish (FIN) AF: 0.610 AC: 6463 AN: 10592

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45447 AN: 68012

Other (OTH) AF: 0.720 AC: 1521 AN: 2112

Alfa AF: 0.654 Hom.: 2722

Bravo AF: 0.721

Asia WGS AF: 0.659 AC: 2292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.19
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs4710189; hg19: chr6-167556324;