6-165065309-A-T

Variant names:

• chr6-165065309-A-T
• rs227453
• ENST00000667740.1:n.270-10915A>T

Variant summary

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

The ENST00000667740.1(ENSG00000287877):​n.270-10915A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 148,890 control chromosomes in the GnomAD database, including 2,846 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 (2846 hom., cov: 32)
• Consequence: ENSG00000287877 ENST00000667740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287877	ENST00000667740.1		n.270-10915A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 26942 AN: 148774 Hom.: 2834 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.181 AC: 26992 AN: 148890 Hom.: 2846 Cov.: 32 AF XY: 0.183 AC XY: 13287 AN XY: 72792

African (AFR) AF: 0.236 AC: 9383 AN: 39786

American (AMR) AF: 0.178 AC: 2627 AN: 14788

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 484 AN: 3412

East Asian (EAS) AF: 0.464 AC: 2352 AN: 5066

South Asian (SAS) AF: 0.209 AC: 973 AN: 4660

European-Finnish (FIN) AF: 0.112 AC: 1176 AN: 10544

Middle Eastern (MID) AF: 0.157 AC: 45 AN: 286

European-Non Finnish (NFE) AF: 0.138 AC: 9309 AN: 67398

Other (OTH) AF: 0.201 AC: 410 AN: 2044

Alfa AF: 0.168 Hom.: 244

Asia WGS AF: 0.336 AC: 1166 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	1.8
DANN	Benign	0.25
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs227453; hg19: chr6-165478798;