5-110161259-T-G

Variant names:

• chr5-110161259-T-G
• rs4460176

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 0.566 in 151,940 control chromosomes in the GnomAD database, including 25,352 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 0.57 (25352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85988 AN: 151820 Hom.: 25350 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.724

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.566 AC: 86024 AN: 151940 Hom.: 25352 Cov.: 32 AF XY: 0.561 AC XY: 41632 AN XY: 74222

African (AFR) AF: 0.425 AC: 17631 AN: 41476

American (AMR) AF: 0.539 AC: 8214 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2646 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1716 AN: 5152

South Asian (SAS) AF: 0.487 AC: 2341 AN: 4808

European-Finnish (FIN) AF: 0.618 AC: 6519 AN: 10550

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.662 AC: 44968 AN: 67932

Other (OTH) AF: 0.586 AC: 1234 AN: 2106

Alfa AF: 0.628 Hom.: 91174

Bravo AF: 0.556

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.9
DANN	Benign	0.81
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4460176; hg19: chr5-109496960;