5-170132706-C-T

Variant names:

• chr5-170132706-C-T
• rs7709558

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 0.72 in 152,128 control chromosomes in the GnomAD database, including 41,248 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 0.72 (41248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.837 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: 0.720 AC: 109446 AN: 152010 Hom.: 41239 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.720 AC: 109491 AN: 152128 Hom.: 41248 Cov.: 32 AF XY: 0.719 AC XY: 53444 AN XY: 74372

African (AFR) AF: 0.486 AC: 20146 AN: 41468

American (AMR) AF: 0.779 AC: 11920 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2847 AN: 3472

East Asian (EAS) AF: 0.526 AC: 2716 AN: 5162

South Asian (SAS) AF: 0.767 AC: 3697 AN: 4822

European-Finnish (FIN) AF: 0.795 AC: 8418 AN: 10588

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57284 AN: 68000

Other (OTH) AF: 0.726 AC: 1535 AN: 2114

Alfa AF: 0.796 Hom.: 32003

Bravo AF: 0.708

Asia WGS AF: 0.656 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.61
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs7709558; hg19: chr5-169559710;