chr6-118359211-C-T

Variant names:

• chr6-118359211-C-T
• rs11970286
• ENST00000778490.1:n.617+38305G>A

Variant summary

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

The ENST00000778490.1(ENSG00000301363):​n.617+38305G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,918 control chromosomes in the GnomAD database, including 10,558 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 0.36 (10558 hom., cov: 31)
• Consequence: ENSG00000301363 ENST00000778490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 56 publications found

Genes affected

ENSG00000301363 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778490.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301363	ENST00000778490.1		n.617+38305G>A		intron	N/A
	ENSG00000301363	ENST00000778491.1		n.159-34024G>A		intron	N/A
	ENSG00000301363	ENST00000778492.1		n.622-35028G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54164 AN: 151800 Hom.: 10561 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.357 AC: 54184 AN: 151918 Hom.: 10558 Cov.: 31 AF XY: 0.353 AC XY: 26184 AN XY: 74258

African (AFR) AF: 0.219 AC: 9058 AN: 41434

American (AMR) AF: 0.260 AC: 3960 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1305 AN: 3464

East Asian (EAS) AF: 0.247 AC: 1280 AN: 5174

South Asian (SAS) AF: 0.385 AC: 1851 AN: 4806

European-Finnish (FIN) AF: 0.437 AC: 4599 AN: 10534

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30957 AN: 67942

Other (OTH) AF: 0.328 AC: 690 AN: 2102

Alfa AF: 0.416 Hom.: 58420

Bravo AF: 0.335

Asia WGS AF: 0.296 AC: 1027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.16
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs11970286; hg19: chr6-118680374;