chr6-117450114-A-T

Variant names:

• chr6-117450114-A-T
• rs17635492
• ENST00000467125.1:c.547+116740T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000467125.1(ENSG00000282218):​c.547+116740T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0241 in 152,368 control chromosomes in the GnomAD database, including 64 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 0.024 (64 hom., cov: 32)
• Consequence: ENSG00000282218 ENST00000467125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 5 publications found

Genes affected

ENSG00000282218 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0241 (3679/152368) while in subpopulation NFE AF = 0.0369 (2512/68040). AF 95% confidence interval is 0.0357. There are 64 homozygotes in GnomAd4. There are 1715 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 64 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000467125.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282218	ENST00000467125.1	TSL:2	c.547+116740T>A		intron	N/A	ENSP00000487717.1

Frequencies

GnomAD3 genomes AF: 0.0242 AC: 3681 AN: 152250 Hom.: 64 Cov.: 32

Gnomad AFR AF: 0.00644

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0144

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.0244

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.0276

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0369

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0241 AC: 3679 AN: 152368 Hom.: 64 Cov.: 32 AF XY: 0.0230 AC XY: 1715 AN XY: 74514

African (AFR) AF: 0.00642 AC: 267 AN: 41588

American (AMR) AF: 0.0144 AC: 220 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0193 AC: 67 AN: 3472

East Asian (EAS) AF: 0.0245 AC: 127 AN: 5190

South Asian (SAS) AF: 0.0120 AC: 58 AN: 4834

European-Finnish (FIN) AF: 0.0276 AC: 293 AN: 10622

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0369 AC: 2512 AN: 68040

Other (OTH) AF: 0.0213 AC: 45 AN: 2112

Alfa AF: 0.0285 Hom.: 5

Bravo AF: 0.0226

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		-0.075

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17635492; hg19: chr6-117771277;