6-164805595-G-A

Variant names:

• chr6-164805595-G-A
• rs1511075
• ENST00000656215.1:n.215+101C>T

Variant summary

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

The ENST00000656215.1(ENSG00000287550):​n.215+101C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 150,706 control chromosomes in the GnomAD database, including 41,541 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 0.73 (41541 hom., cov: 28)
• Consequence: ENSG00000287550 ENST00000656215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 1 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.887 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.160+101C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287550	ENST00000656215.1		n.215+101C>T		intron	N/A
	ENSG00000287550	ENST00000656968.1		n.640+101C>T		intron	N/A
	ENSG00000287550	ENST00000662461.1		n.374+101C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.734 AC: 110541 AN: 150592 Hom.: 41524 Cov.: 28

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.734 AC: 110588 AN: 150706 Hom.: 41541 Cov.: 28 AF XY: 0.741 AC XY: 54552 AN XY: 73654

African (AFR) AF: 0.555 AC: 22611 AN: 40760

American (AMR) AF: 0.793 AC: 12037 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2806 AN: 3464

East Asian (EAS) AF: 0.895 AC: 4552 AN: 5088

South Asian (SAS) AF: 0.910 AC: 4363 AN: 4796

European-Finnish (FIN) AF: 0.845 AC: 8799 AN: 10418

Middle Eastern (MID) AF: 0.731 AC: 212 AN: 290

European-Non Finnish (NFE) AF: 0.782 AC: 52927 AN: 67710

Other (OTH) AF: 0.760 AC: 1601 AN: 2106

Alfa AF: 0.685 Hom.: 2076

Bravo AF: 0.719

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.38
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1511075; hg19: chr6-165219084;