6-165052862-T-C

Variant names:

• chr6-165052862-T-C
• rs227458
• ENST00000667740.1:n.270-23362T>C

Variant summary

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

The ENST00000667740.1(ENSG00000287877):​n.270-23362T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,218 control chromosomes in the GnomAD database, including 63,770 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 0.91 (63770 hom., cov: 31)
• Consequence: ENSG00000287877 ENST00000667740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 5 publications found

Genes affected

ENSG00000287877 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287877	ENST00000667740.1	n.270-23362T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.914 AC: 139022 AN: 152100 Hom.: 63712 Cov.: 31

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.914 AC: 139139 AN: 152218 Hom.: 63770 Cov.: 31 AF XY: 0.914 AC XY: 68007 AN XY: 74414

African (AFR) AF: 0.978 AC: 40637 AN: 41548

American (AMR) AF: 0.898 AC: 13735 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3187 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5140 AN: 5166

South Asian (SAS) AF: 0.918 AC: 4434 AN: 4830

European-Finnish (FIN) AF: 0.899 AC: 9512 AN: 10586

Middle Eastern (MID) AF: 0.945 AC: 276 AN: 292

European-Non Finnish (NFE) AF: 0.875 AC: 59472 AN: 68004

Other (OTH) AF: 0.916 AC: 1936 AN: 2114

Alfa AF: 0.896 Hom.: 88986

Bravo AF: 0.917

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.67
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs227458; hg19: chr6-165466351;