rs2732167

Positions:

• chr4-87785141-A-G
• chr4-87785141-A-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 0.93 in 152,200 control chromosomes in the GnomAD database, including 66,048 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 0.93 (66048 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141493 AN: 152082 Hom.: 65991 Cov.: 31

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.929

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

GnomAD4 genome AF: 0.930 AC: 141609 AN: 152200 Hom.: 66048 Cov.: 31 AF XY: 0.932 AC XY: 69338 AN XY: 74392

Gnomad4 AFR AF: 0.982

Gnomad4 AMR AF: 0.963

Gnomad4 ASJ AF: 0.957

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.944

Gnomad4 FIN AF: 0.880

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.930

Alfa AF: 0.904 Hom.: 34665

Bravo AF: 0.940

Asia WGS AF: 0.972 AC: 3381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.066
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2732167; hg19: chr4-88706293;