rs2170568

Variant names:

• chr8-129808129-T-A
• rs2170568

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 0.149 in 152,246 control chromosomes in the GnomAD database, including 1,746 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 0.15 (1746 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 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: 0.149 AC: 22699 AN: 152128 Hom.: 1745 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.149 AC: 22710 AN: 152246 Hom.: 1746 Cov.: 33 AF XY: 0.148 AC XY: 11032 AN XY: 74444

African (AFR) AF: 0.119 AC: 4936 AN: 41570

American (AMR) AF: 0.142 AC: 2171 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1001 AN: 3470

East Asian (EAS) AF: 0.106 AC: 547 AN: 5176

South Asian (SAS) AF: 0.154 AC: 744 AN: 4822

European-Finnish (FIN) AF: 0.108 AC: 1149 AN: 10606

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11608 AN: 67988

Other (OTH) AF: 0.178 AC: 375 AN: 2112

Alfa AF: 0.157 Hom.: 242

Bravo AF: 0.149

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.67
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2170568; hg19: chr8-130820375;