chr5-177104771-A-G

Variant names:

• chr5-177104771-A-G
• rs7708357

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 0.592 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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.406 AC: 16804 AN: 41406

American (AMR) AF: 0.683 AC: 10401 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2337 AN: 3472

East Asian (EAS) AF: 0.957 AC: 4947 AN: 5170

South Asian (SAS) AF: 0.809 AC: 3898 AN: 4816

European-Finnish (FIN) AF: 0.674 AC: 7120 AN: 10558

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42547 AN: 67926

Other (OTH) AF: 0.591 AC: 1246 AN: 2110

Alfa AF: 0.596 Hom.: 39443

Bravo AF: 0.582

Asia WGS AF: 0.786 AC: 2735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.69
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs7708357; hg19: chr5-176531772;