rs2170096

Variant names:

• chr8-144447145-C-G
• rs2170096

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 0.499 in 152,036 control chromosomes in the GnomAD database, including 19,074 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 0.50 (19074 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.557 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: 0.499 AC: 75859 AN: 151914 Hom.: 19077 Cov.: 33

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.499 AC: 75882 AN: 152036 Hom.: 19074 Cov.: 33 AF XY: 0.500 AC XY: 37128 AN XY: 74310

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.509

Alfa AF: 0.504 Hom.: 2411

Bravo AF: 0.493

Asia WGS AF: 0.508 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2170096; hg19: chr8-145672528;