5-176520050-C-T

Variant names:

• chr5-176520050-C-T
• rs4868644

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 0.49 in 152,090 control chromosomes in the GnomAD database, including 18,387 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 0.49 (18387 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.515 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: 0.490 AC: 74528 AN: 151972 Hom.: 18377 Cov.: 33

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.490 AC: 74562 AN: 152090 Hom.: 18387 Cov.: 33 AF XY: 0.489 AC XY: 36373 AN XY: 74364

African (AFR) AF: 0.459 AC: 19045 AN: 41510

American (AMR) AF: 0.525 AC: 8025 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2355 AN: 5178

South Asian (SAS) AF: 0.399 AC: 1922 AN: 4814

European-Finnish (FIN) AF: 0.549 AC: 5797 AN: 10566

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33778 AN: 67944

Other (OTH) AF: 0.495 AC: 1048 AN: 2116

Alfa AF: 0.494 Hom.: 82592

Bravo AF: 0.490

Asia WGS AF: 0.453 AC: 1575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.033
DANN	Benign	0.59
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4868644; hg19: chr5-175947051;