5-8174936-C-T

Variant names:

• chr5-8174936-C-T
• rs901893

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 0.59 in 152,076 control chromosomes in the GnomAD database, including 27,977 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 (27977 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 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: 0.590 AC: 89678 AN: 151958 Hom.: 27968 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.590 AC: 89701 AN: 152076 Hom.: 27977 Cov.: 33 AF XY: 0.596 AC XY: 44293 AN XY: 74346

African (AFR) AF: 0.383 AC: 15896 AN: 41466

American (AMR) AF: 0.616 AC: 9404 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2084 AN: 3472

East Asian (EAS) AF: 0.839 AC: 4321 AN: 5152

South Asian (SAS) AF: 0.631 AC: 3040 AN: 4820

European-Finnish (FIN) AF: 0.748 AC: 7929 AN: 10598

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45074 AN: 67978

Other (OTH) AF: 0.586 AC: 1237 AN: 2110

Alfa AF: 0.633 Hom.: 52130

Bravo AF: 0.575

Asia WGS AF: 0.688 AC: 2391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.58
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs901893; hg19: chr5-8175049;