6-113158133-G-T

Variant names:

• chr6-113158133-G-T
• rs2473967
• ENST00000722487.1:n.140-15213G>T

Variant summary

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

The ENST00000722487.1(ENSG00000287728):​n.140-15213G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,188 control chromosomes in the GnomAD database, including 61,198 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 0.89 (61198 hom., cov: 33)
• Consequence: ENSG00000287728 ENST00000722487.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 9 publications found

Genes affected

ENSG00000287728 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722487.1. 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
	ENSG00000287728	ENST00000722487.1		n.140-15213G>T		intron	N/A
	ENSG00000287728	ENST00000722488.1		n.437-15213G>T		intron	N/A
	ENSG00000287728	ENST00000722489.1		n.83-15213G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136089 AN: 152070 Hom.: 61147 Cov.: 33

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.947

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.895 AC: 136199 AN: 152188 Hom.: 61198 Cov.: 33 AF XY: 0.892 AC XY: 66380 AN XY: 74388

African (AFR) AF: 0.820 AC: 34029 AN: 41504

American (AMR) AF: 0.946 AC: 14465 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3338 AN: 3472

East Asian (EAS) AF: 0.848 AC: 4385 AN: 5172

South Asian (SAS) AF: 0.848 AC: 4093 AN: 4826

European-Finnish (FIN) AF: 0.870 AC: 9207 AN: 10584

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.935 AC: 63600 AN: 68024

Other (OTH) AF: 0.926 AC: 1959 AN: 2116

Alfa AF: 0.922 Hom.: 153611

Bravo AF: 0.900

Asia WGS AF: 0.853 AC: 2945 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.8
DANN	Benign	0.52
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs2473967; hg19: chr6-113479335;