chr6-142550741-G-A

Variant names:

• chr6-142550741-G-A
• rs839556
• ENST00000447311.1:n.178-5748C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000447311.1(ENSG00000236366):​n.178-5748C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,056 control chromosomes in the GnomAD database, including 19,488 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 0.48 (19488 hom., cov: 33)
• Consequence: ENSG00000236366 ENST00000447311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 8 publications found

Genes affected

ENSG00000236366 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447311.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC153910	NR_027311.1		n.362-22358C>T		intron	N/A
	LOC153910	NR_027312.1		n.178-5748C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236366	ENST00000447311.1	TSL:2	n.178-5748C>T		intron	N/A
	ENSG00000236366	ENST00000635073.1	TSL:4	n.301-5748C>T		intron	N/A
	ENSG00000236366	ENST00000817224.1		n.311+841C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72238 AN: 151938 Hom.: 19482 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.475 AC: 72263 AN: 152056 Hom.: 19488 Cov.: 33 AF XY: 0.481 AC XY: 35747 AN XY: 74370

African (AFR) AF: 0.204 AC: 8456 AN: 41454

American (AMR) AF: 0.616 AC: 9418 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1888 AN: 3468

East Asian (EAS) AF: 0.724 AC: 3747 AN: 5174

South Asian (SAS) AF: 0.559 AC: 2692 AN: 4816

European-Finnish (FIN) AF: 0.594 AC: 6271 AN: 10564

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38204 AN: 67978

Other (OTH) AF: 0.470 AC: 992 AN: 2112

Alfa AF: 0.540 Hom.: 12836

Bravo AF: 0.463

Asia WGS AF: 0.567 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.57
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs839556; hg19: chr6-142871878;