2-170102172-T-G

Variant names:

• chr2-170102172-T-G
• rs6711417

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 0.175 in 152,138 control chromosomes in the GnomAD database, including 2,570 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 0.18 (2570 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26642 AN: 152020 Hom.: 2569 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.175 AC: 26650 AN: 152138 Hom.: 2570 Cov.: 32 AF XY: 0.179 AC XY: 13316 AN XY: 74360

African (AFR) AF: 0.156 AC: 6472 AN: 41516

American (AMR) AF: 0.176 AC: 2684 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 854 AN: 3468

East Asian (EAS) AF: 0.365 AC: 1887 AN: 5174

South Asian (SAS) AF: 0.326 AC: 1571 AN: 4820

European-Finnish (FIN) AF: 0.159 AC: 1681 AN: 10582

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10948 AN: 67992

Other (OTH) AF: 0.163 AC: 344 AN: 2106

Alfa AF: 0.170 Hom.: 410

Bravo AF: 0.174

Asia WGS AF: 0.357 AC: 1241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.1
DANN	Benign	0.61
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs6711417; hg19: chr2-170958682;