chr6-68475863-G-A

Variant names:

• chr6-68475863-G-A
• rs1565488
• ENST00000654495.1:n.235+36926C>T

Variant summary

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

The ENST00000654495.1(ENSG00000288088):​n.235+36926C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 151,750 control chromosomes in the GnomAD database, including 39,369 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 0.71 (39369 hom., cov: 30)
• Consequence: ENSG00000288088 ENST00000654495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 0 publications found

Genes affected

ENSG00000288088 (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 = 0.822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654495.1. 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
	ENSG00000288088	ENST00000654495.1		n.235+36926C>T		intron	N/A
	ENSG00000288088	ENST00000657302.1		n.111+100182C>T		intron	N/A
	ENSG00000288088	ENST00000669267.1		n.86-8614C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108191 AN: 151632 Hom.: 39352 Cov.: 30

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.713 AC: 108255 AN: 151750 Hom.: 39369 Cov.: 30 AF XY: 0.715 AC XY: 52999 AN XY: 74162

African (AFR) AF: 0.557 AC: 23074 AN: 41390

American (AMR) AF: 0.735 AC: 11222 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2884 AN: 3464

East Asian (EAS) AF: 0.843 AC: 4329 AN: 5136

South Asian (SAS) AF: 0.764 AC: 3673 AN: 4810

European-Finnish (FIN) AF: 0.750 AC: 7888 AN: 10514

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52684 AN: 67864

Other (OTH) AF: 0.745 AC: 1567 AN: 2102

Alfa AF: 0.752 Hom.: 17792

Bravo AF: 0.705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.39
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1565488; hg19: chr6-69185755; COSMIC: COSV69403346;