6-165064562-T-C

Variant names:

• chr6-165064562-T-C
• rs227455
• ENST00000667740.1:n.270-11662T>C

Variant summary

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

The ENST00000667740.1(ENSG00000287877):​n.270-11662T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,116 control chromosomes in the GnomAD database, including 2,860 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 0.18 (2860 hom., cov: 31)
• Consequence: ENSG00000287877 ENST00000667740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667740.1. 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
	ENSG00000287877	ENST00000667740.1		n.270-11662T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27064 AN: 151998 Hom.: 2848 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.178 AC: 27116 AN: 152116 Hom.: 2860 Cov.: 31 AF XY: 0.179 AC XY: 13347 AN XY: 74376

African (AFR) AF: 0.227 AC: 9401 AN: 41492

American (AMR) AF: 0.172 AC: 2636 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 491 AN: 3472

East Asian (EAS) AF: 0.458 AC: 2360 AN: 5152

South Asian (SAS) AF: 0.204 AC: 981 AN: 4820

European-Finnish (FIN) AF: 0.111 AC: 1173 AN: 10592

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9378 AN: 67994

Other (OTH) AF: 0.197 AC: 416 AN: 2110

Alfa AF: 0.155 Hom.: 6696

Bravo AF: 0.183

Asia WGS AF: 0.340 AC: 1181 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	1.2
DANN	Benign	0.37
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs227455; hg19: chr6-165478051;