2-170876715-G-C

Position:

• chr2-170876715-G-C

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 0.909 in 152,132 control chromosomes in the GnomAD database, including 63,611 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 0.91 (63611 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

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 (NFE) allele frequency at 95% confidence interval = 0.973 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: 0.909 AC: 138182 AN: 152016 Hom.: 63569 Cov.: 31

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.909 AC: 138281 AN: 152132 Hom.: 63611 Cov.: 31 AF XY: 0.911 AC XY: 67731 AN XY: 74368

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.946

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.970

Gnomad4 FIN AF: 0.994

Gnomad4 NFE AF: 0.979

Gnomad4 OTH AF: 0.916

Alfa AF: 0.961 Hom.: 38558

Bravo AF: 0.895

Asia WGS AF: 0.902 AC: 3135 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	5.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4668338; hg19: chr2-171733225;