rs267071

Variant names:

• chr5-117612808-G-A
• rs267071

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 0.454 in 152,088 control chromosomes in the GnomAD database, including 20,271 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 0.45 (20271 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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: 0.454 AC: 68972 AN: 151972 Hom.: 20228 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.0411

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.454 AC: 69069 AN: 152088 Hom.: 20271 Cov.: 33 AF XY: 0.447 AC XY: 33212 AN XY: 74328

African (AFR) AF: 0.836 AC: 34737 AN: 41538

American (AMR) AF: 0.300 AC: 4589 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1171 AN: 3470

East Asian (EAS) AF: 0.0410 AC: 212 AN: 5170

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4818

European-Finnish (FIN) AF: 0.287 AC: 3026 AN: 10530

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22496 AN: 67956

Other (OTH) AF: 0.426 AC: 900 AN: 2112

Alfa AF: 0.429 Hom.: 2187

Bravo AF: 0.468

Asia WGS AF: 0.228 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.67
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs267071; hg19: chr5-116948503;