6-153991251-C-T

Variant names:

• chr6-153991251-C-T
• rs12527423

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 0.164 in 152,148 control chromosomes in the GnomAD database, including 2,596 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 (2596 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 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: 0.164 AC: 24945 AN: 152032 Hom.: 2599 Cov.: 32

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.164 AC: 24940 AN: 152148 Hom.: 2596 Cov.: 32 AF XY: 0.175 AC XY: 13035 AN XY: 74370

African (AFR) AF: 0.0540 AC: 2243 AN: 41536

American (AMR) AF: 0.255 AC: 3898 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3468

East Asian (EAS) AF: 0.370 AC: 1911 AN: 5168

South Asian (SAS) AF: 0.363 AC: 1748 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2454 AN: 10584

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11425 AN: 67986

Other (OTH) AF: 0.175 AC: 369 AN: 2110

Alfa AF: 0.159 Hom.: 294

Bravo AF: 0.154

Asia WGS AF: 0.366 AC: 1272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.6
DANN	Benign	0.73
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs12527423; hg19: chr6-154312386;