chr6-153947409-C-T

Variant names:

• chr6-153947409-C-T
• rs1033816

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 0.254 in 151,638 control chromosomes in the GnomAD database, including 5,119 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 0.25 (5119 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38531 AN: 151520 Hom.: 5106 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.254 AC: 38550 AN: 151638 Hom.: 5119 Cov.: 32 AF XY: 0.263 AC XY: 19475 AN XY: 74050

African (AFR) AF: 0.234 AC: 9662 AN: 41372

American (AMR) AF: 0.404 AC: 6152 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 928 AN: 3468

East Asian (EAS) AF: 0.334 AC: 1723 AN: 5158

South Asian (SAS) AF: 0.392 AC: 1886 AN: 4808

European-Finnish (FIN) AF: 0.265 AC: 2758 AN: 10420

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14549 AN: 67870

Other (OTH) AF: 0.279 AC: 586 AN: 2102

Alfa AF: 0.235 Hom.: 553

Bravo AF: 0.257

Asia WGS AF: 0.386 AC: 1340 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.47
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1033816; hg19: chr6-154268544; COSMIC: COSV107167846;