chr2-170876715-G-C

Variant names:

• chr2-170876715-G-C
• rs4668338

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;