rs1877632

Variant names:

• chr17-43722222-G-A
• rs1877632

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 0.312 in 152,112 control chromosomes in the GnomAD database, including 7,557 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 0.31 (7557 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 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: 0.312 AC: 47456 AN: 151994 Hom.: 7558 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.312 AC: 47470 AN: 152112 Hom.: 7557 Cov.: 32 AF XY: 0.316 AC XY: 23497 AN XY: 74356

African (AFR) AF: 0.268 AC: 11136 AN: 41486

American (AMR) AF: 0.285 AC: 4361 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1345 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1082 AN: 5170

South Asian (SAS) AF: 0.290 AC: 1400 AN: 4824

European-Finnish (FIN) AF: 0.456 AC: 4824 AN: 10568

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22296 AN: 67994

Other (OTH) AF: 0.295 AC: 622 AN: 2112

Alfa AF: 0.318 Hom.: 33426

Bravo AF: 0.299

Asia WGS AF: 0.214 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.64
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs1877632; hg19: chr17-41799590;