5-71816880-G-C

Variant names:

• chr5-71816880-G-C
• rs2251262

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 0.349 in 152,048 control chromosomes in the GnomAD database, including 9,734 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 0.35 (9734 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 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: 0.349 AC: 52948 AN: 151930 Hom.: 9707 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.349 AC: 53023 AN: 152048 Hom.: 9734 Cov.: 32 AF XY: 0.356 AC XY: 26422 AN XY: 74310

African (AFR) AF: 0.339 AC: 14058 AN: 41462

American (AMR) AF: 0.445 AC: 6800 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3009 AN: 5146

South Asian (SAS) AF: 0.548 AC: 2638 AN: 4810

European-Finnish (FIN) AF: 0.269 AC: 2846 AN: 10578

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21455 AN: 67976

Other (OTH) AF: 0.357 AC: 754 AN: 2114

Alfa AF: 0.160 Hom.: 257

Bravo AF: 0.359

Asia WGS AF: 0.532 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.81
DANN	Benign	0.71
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2251262; hg19: chr5-71112707;