chr4-154622217-T-C

Variant names:

• chr4-154622217-T-C
• rs6536024

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 0.465 in 152,006 control chromosomes in the GnomAD database, including 17,014 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 0.47 (17014 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• Publications: 21 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 = 0.6 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: 0.466 AC: 70721 AN: 151888 Hom.: 17016 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.465 AC: 70738 AN: 152006 Hom.: 17014 Cov.: 32 AF XY: 0.464 AC XY: 34461 AN XY: 74278

African (AFR) AF: 0.355 AC: 14715 AN: 41452

American (AMR) AF: 0.398 AC: 6070 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1448 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3185 AN: 5154

South Asian (SAS) AF: 0.480 AC: 2313 AN: 4816

European-Finnish (FIN) AF: 0.496 AC: 5244 AN: 10562

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36269 AN: 67978

Other (OTH) AF: 0.446 AC: 941 AN: 2112

Alfa AF: 0.507 Hom.: 35335

Bravo AF: 0.456

Asia WGS AF: 0.509 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.75
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs6536024; hg19: chr4-155543369;