6-153946269-C-T

Variant names:

• chr6-153946269-C-T
• rs1033817

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 0.374 in 152,068 control chromosomes in the GnomAD database, including 10,880 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 0.37 (10880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• 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 = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56881 AN: 151950 Hom.: 10853 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.374 AC: 56949 AN: 152068 Hom.: 10880 Cov.: 32 AF XY: 0.380 AC XY: 28290 AN XY: 74368

African (AFR) AF: 0.419 AC: 17356 AN: 41466

American (AMR) AF: 0.475 AC: 7269 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1504 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2581 AN: 5162

South Asian (SAS) AF: 0.480 AC: 2314 AN: 4820

European-Finnish (FIN) AF: 0.310 AC: 3275 AN: 10576

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21437 AN: 67964

Other (OTH) AF: 0.390 AC: 824 AN: 2112

Alfa AF: 0.222 Hom.: 475

Bravo AF: 0.383

Asia WGS AF: 0.544 AC: 1891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.023
DANN	Benign	0.21
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1033817; hg19: chr6-154267404;