rs2170096

Variant names:

• chr8-144447145-C-G
• rs2170096

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.536 AC: 22219 AN: 41466

American (AMR) AF: 0.445 AC: 6796 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3468

East Asian (EAS) AF: 0.390 AC: 2010 AN: 5158

South Asian (SAS) AF: 0.575 AC: 2770 AN: 4816

European-Finnish (FIN) AF: 0.548 AC: 5786 AN: 10566

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33015 AN: 67970

Other (OTH) AF: 0.509 AC: 1072 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.56
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2170096; hg19: chr8-145672528;