rs4710189

Positions:

• chr6-167142836-G-A
• chr6-167142836-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.720

Alfa AF: 0.643 Hom.: 2470

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4710189; hg19: chr6-167556324;