6-44266184-C-T

Variant names:

• chr6-44266184-C-T
• rs2233424

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 0.0519 in 152,296 control chromosomes in the GnomAD database, including 272 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 0.052 (272 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 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: 0.0519 AC: 7894 AN: 152178 Hom.: 272 Cov.: 33

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0796

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0405

Gnomad OTH AF: 0.0420

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

GnomAD4 genome AF: 0.0519 AC: 7904 AN: 152296 Hom.: 272 Cov.: 33 AF XY: 0.0529 AC XY: 3943 AN XY: 74472

African (AFR) AF: 0.0588 AC: 2442 AN: 41554

American (AMR) AF: 0.0456 AC: 698 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0205 AC: 71 AN: 3470

East Asian (EAS) AF: 0.171 AC: 887 AN: 5182

South Asian (SAS) AF: 0.0176 AC: 85 AN: 4832

European-Finnish (FIN) AF: 0.0796 AC: 845 AN: 10616

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0405 AC: 2754 AN: 68024

Other (OTH) AF: 0.0435 AC: 92 AN: 2116

Alfa AF: 0.0480 Hom.: 399

Bravo AF: 0.0512

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.65
PhyloP100		-0.52
PromoterAI		-0.029	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2233424; hg19: chr6-44233921;