rs1862175

Variant names:

• chr5-122197166-T-C
• rs1862175

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 0.426 in 152,020 control chromosomes in the GnomAD database, including 16,345 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 0.43 (16345 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 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: 0.426 AC: 64640 AN: 151902 Hom.: 16293 Cov.: 33

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.426 AC: 64759 AN: 152020 Hom.: 16345 Cov.: 33 AF XY: 0.430 AC XY: 31913 AN XY: 74300

African (AFR) AF: 0.703 AC: 29137 AN: 41448

American (AMR) AF: 0.390 AC: 5954 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1113 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1505 AN: 5156

South Asian (SAS) AF: 0.440 AC: 2120 AN: 4816

European-Finnish (FIN) AF: 0.379 AC: 4016 AN: 10588

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19706 AN: 67966

Other (OTH) AF: 0.401 AC: 847 AN: 2114

Alfa AF: 0.371 Hom.: 5327

Bravo AF: 0.439

Asia WGS AF: 0.436 AC: 1517 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	1.9
DANN	Benign	0.38
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1862175; hg19: chr5-121532861;