chr5-175435192-C-T

Variant names:

• chr5-175435192-C-T
• rs265975

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.428 in 151,974 control chromosomes in the GnomAD database, including 15,283 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 0.43 (15283 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 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: 0.428 AC: 64944 AN: 151856 Hom.: 15263 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.428 AC: 65009 AN: 151974 Hom.: 15283 Cov.: 31 AF XY: 0.422 AC XY: 31333 AN XY: 74268

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.408

Alfa AF: 0.394 Hom.: 3433

Bravo AF: 0.445

Asia WGS AF: 0.356 AC: 1238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs265975; hg19: chr5-174862195;