rs2177549

Variant names:

• chr7-54116368-G-T
• rs2177549

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 0.192 in 152,084 control chromosomes in the GnomAD database, including 2,858 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 0.19 (2858 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.197 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: 0.192 AC: 29104 AN: 151966 Hom.: 2853 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0503

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.192 AC: 29138 AN: 152084 Hom.: 2858 Cov.: 32 AF XY: 0.194 AC XY: 14446 AN XY: 74346

African (AFR) AF: 0.191 AC: 7926 AN: 41456

American (AMR) AF: 0.203 AC: 3105 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3468

East Asian (EAS) AF: 0.0503 AC: 260 AN: 5172

South Asian (SAS) AF: 0.159 AC: 767 AN: 4812

European-Finnish (FIN) AF: 0.223 AC: 2365 AN: 10594

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13554 AN: 67978

Other (OTH) AF: 0.156 AC: 329 AN: 2114

Alfa AF: 0.196 Hom.: 1516

Bravo AF: 0.191

Asia WGS AF: 0.139 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.52
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs2177549; hg19: chr7-54184061;