5-149644288-T-C

Variant names:

• chr5-149644288-T-C
• rs10069462

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 0.16 in 152,152 control chromosomes in the GnomAD database, including 2,189 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 0.16 (2189 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.256 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: 0.160 AC: 24335 AN: 152034 Hom.: 2189 Cov.: 32

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.160 AC: 24342 AN: 152152 Hom.: 2189 Cov.: 32 AF XY: 0.164 AC XY: 12174 AN XY: 74370

African (AFR) AF: 0.0834 AC: 3464 AN: 41534

American (AMR) AF: 0.132 AC: 2019 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1381 AN: 5166

South Asian (SAS) AF: 0.207 AC: 996 AN: 4822

European-Finnish (FIN) AF: 0.246 AC: 2593 AN: 10562

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12587 AN: 67996

Other (OTH) AF: 0.171 AC: 360 AN: 2108

Alfa AF: 0.163 Hom.: 332

Bravo AF: 0.144

Asia WGS AF: 0.252 AC: 875 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	2.8
DANN	Benign	0.36
PhyloP100		-0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10069462;

hg19: chr5-149023851;