5-75269328-C-T

Variant names:

• chr5-75269328-C-T
• rs10062361

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 0.197 in 143,840 control chromosomes in the GnomAD database, including 3,193 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 0.20 (3193 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.315 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: 0.197 AC: 28381 AN: 143734 Hom.: 3195 Cov.: 28

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.129

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.197 AC: 28376 AN: 143840 Hom.: 3193 Cov.: 28 AF XY: 0.203 AC XY: 14193 AN XY: 70058

African (AFR) AF: 0.135 AC: 5354 AN: 39562

American (AMR) AF: 0.204 AC: 2926 AN: 14368

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 819 AN: 3236

East Asian (EAS) AF: 0.290 AC: 1371 AN: 4720

South Asian (SAS) AF: 0.329 AC: 1454 AN: 4424

European-Finnish (FIN) AF: 0.272 AC: 2611 AN: 9602

Middle Eastern (MID) AF: 0.129 AC: 36 AN: 280

European-Non Finnish (NFE) AF: 0.204 AC: 13198 AN: 64780

Other (OTH) AF: 0.172 AC: 345 AN: 2000

Alfa AF: 0.214 Hom.: 4401

Bravo AF: 0.201

Asia WGS AF: 0.182 AC: 543 AN: 2986

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.5
DANN	Benign	0.83

Splicing

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

Other links and lift over

dbSNP: rs10062361; hg19: chr5-74565153;