rs2177189

Variant names:

• chr7-150566235-G-A
• rs2177189

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 0.141 in 152,116 control chromosomes in the GnomAD database, including 1,796 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 0.14 (1796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 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: 0.141 AC: 21453 AN: 151998 Hom.: 1798 Cov.: 32

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.141 AC: 21458 AN: 152116 Hom.: 1796 Cov.: 32 AF XY: 0.142 AC XY: 10560 AN XY: 74366

African (AFR) AF: 0.0529 AC: 2196 AN: 41498

American (AMR) AF: 0.151 AC: 2306 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1056 AN: 5176

South Asian (SAS) AF: 0.147 AC: 706 AN: 4818

European-Finnish (FIN) AF: 0.204 AC: 2160 AN: 10566

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12131 AN: 67970

Other (OTH) AF: 0.158 AC: 334 AN: 2112

Alfa AF: 0.161 Hom.: 2403

Bravo AF: 0.133

Asia WGS AF: 0.177 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.0
DANN	Benign	0.50
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2177189; hg19: chr7-150263323;