5-177104771-A-G

Variant names:

• chr5-177104771-A-G
• rs7708357

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 0.592 in 151,896 control chromosomes in the GnomAD database, including 28,057 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 0.59 (28057 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 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: 0.593 AC: 89936 AN: 151778 Hom.: 28040 Cov.: 31

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.592 AC: 89989 AN: 151896 Hom.: 28057 Cov.: 31 AF XY: 0.601 AC XY: 44606 AN XY: 74208

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.591

Alfa AF: 0.611 Hom.: 26560

Bravo AF: 0.582

Asia WGS AF: 0.786 AC: 2735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7708357; hg19: chr5-176531772;