rs263178

Variant names:

• chr6-142543969-C-T
• rs263178
• ENST00000447311.1:n.364+838G>A

Variant summary

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

The ENST00000447311.1(ENSG00000236366):​n.364+838G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,024 control chromosomes in the GnomAD database, including 8,460 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 0.33 (8460 hom., cov: 32)
• Consequence: ENSG00000236366 ENST00000447311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 9 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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 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.362-15586G>A		intron	N/A
	LOC153910	NR_027312.1		n.364+838G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236366	ENST00000447311.1	TSL:2	n.364+838G>A		intron	N/A
	ENSG00000236366	ENST00000635073.1	TSL:4	n.487+838G>A		intron	N/A
	ENSG00000236366	ENST00000817224.1		n.311+7613G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50311 AN: 151906 Hom.: 8444 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.331 AC: 50367 AN: 152024 Hom.: 8460 Cov.: 32 AF XY: 0.331 AC XY: 24615 AN XY: 74292

African (AFR) AF: 0.399 AC: 16511 AN: 41422

American (AMR) AF: 0.338 AC: 5172 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1189 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1849 AN: 5172

South Asian (SAS) AF: 0.343 AC: 1654 AN: 4820

European-Finnish (FIN) AF: 0.270 AC: 2846 AN: 10558

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19984 AN: 67978

Other (OTH) AF: 0.372 AC: 785 AN: 2110

Alfa AF: 0.307 Hom.: 4623

Bravo AF: 0.336

Asia WGS AF: 0.394 AC: 1368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.1
DANN	Benign	0.80
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs263178; hg19: chr6-142865106;