8-48494802-C-T

Variant names:

• chr8-48494802-C-T
• rs1910252

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 0.232 in 152,154 control chromosomes in the GnomAD database, including 4,699 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 0.23 (4699 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.344 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: 0.232 AC: 35339 AN: 152036 Hom.: 4692 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.232 AC: 35368 AN: 152154 Hom.: 4699 Cov.: 32 AF XY: 0.231 AC XY: 17187 AN XY: 74382

African (AFR) AF: 0.349 AC: 14460 AN: 41486

American (AMR) AF: 0.210 AC: 3212 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3468

East Asian (EAS) AF: 0.237 AC: 1228 AN: 5174

South Asian (SAS) AF: 0.259 AC: 1252 AN: 4826

European-Finnish (FIN) AF: 0.122 AC: 1297 AN: 10588

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11763 AN: 68018

Other (OTH) AF: 0.256 AC: 540 AN: 2112

Alfa AF: 0.0959 Hom.: 144

Bravo AF: 0.244

Asia WGS AF: 0.291 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.050
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: rs1910252; hg19: chr8-49407362;