5-175436902-C-T

Variant names:

• chr5-175436902-C-T
• rs265978

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 0.651 in 151,398 control chromosomes in the GnomAD database, including 32,355 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 0.65 (32355 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98412 AN: 151284 Hom.: 32327 Cov.: 29

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.651 AC: 98498 AN: 151398 Hom.: 32355 Cov.: 29 AF XY: 0.653 AC XY: 48272 AN XY: 73924

African (AFR) AF: 0.681 AC: 28100 AN: 41276

American (AMR) AF: 0.710 AC: 10796 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2388 AN: 3462

East Asian (EAS) AF: 0.851 AC: 4375 AN: 5142

South Asian (SAS) AF: 0.580 AC: 2769 AN: 4778

European-Finnish (FIN) AF: 0.621 AC: 6470 AN: 10414

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41481 AN: 67808

Other (OTH) AF: 0.675 AC: 1416 AN: 2098

Alfa AF: 0.632 Hom.: 50652

Bravo AF: 0.664

Asia WGS AF: 0.698 AC: 2425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs265978; hg19: chr5-174863905;