ENST00000656215.1:n.354-1809C>A

Variant names:

• chr6-164795961-G-T
• rs1877165
• ENST00000656215.1:n.354-1809C>A

Variant summary

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

The ENST00000656215.1(ENSG00000287550):​n.354-1809C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,986 control chromosomes in the GnomAD database, including 5,287 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 0.26 (5287 hom., cov: 32)
• Consequence: ENSG00000287550 ENST00000656215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 2 publications found

Genes affected

ENSG00000287550 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656215.1. 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
	MEAT6	NR_131926.1		n.296-1809C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287550	ENST00000656215.1		n.354-1809C>A		intron	N/A
	ENSG00000287550	ENST00000656968.1		n.776-1809C>A		intron	N/A
	ENSG00000287550	ENST00000662461.1		n.513-1809C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38749 AN: 151868 Hom.: 5266 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.255 AC: 38792 AN: 151986 Hom.: 5287 Cov.: 32 AF XY: 0.259 AC XY: 19264 AN XY: 74280

African (AFR) AF: 0.275 AC: 11397 AN: 41436

American (AMR) AF: 0.326 AC: 4987 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 677 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2030 AN: 5142

South Asian (SAS) AF: 0.432 AC: 2082 AN: 4820

European-Finnish (FIN) AF: 0.207 AC: 2183 AN: 10552

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14675 AN: 67970

Other (OTH) AF: 0.258 AC: 545 AN: 2114

Alfa AF: 0.250 Hom.: 816

Bravo AF: 0.265

Asia WGS AF: 0.431 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.90
DANN	Benign	0.61
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1877165; hg19: chr6-165209450;