chr5-170132706-C-T

Variant names:

• chr5-170132706-C-T
• rs7709558

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.820

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.726

Alfa AF: 0.811 Hom.: 21809

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7709558; hg19: chr5-169559710;