6-68432116-T-G

Variant names:

• chr6-68432116-T-G
• rs9363918
• ENST00000654495.1:n.235+80673A>C

Variant summary

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

The ENST00000654495.1(ENSG00000288088):​n.235+80673A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,658 control chromosomes in the GnomAD database, including 12,284 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 0.39 (12284 hom., cov: 30)
• Consequence: ENSG00000288088 ENST00000654495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 11 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288088	ENST00000654495.1	n.235+80673A>C		intron_variant	Intron 2 of 3
ENSG00000288088	ENST00000657302.1	n.112-90596A>C		intron_variant	Intron 1 of 2
ENSG00000288088	ENST00000669267.1	n.168+35051A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58468 AN: 151540 Hom.: 12272 Cov.: 30

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.386 AC: 58509 AN: 151658 Hom.: 12284 Cov.: 30 AF XY: 0.391 AC XY: 28953 AN XY: 74102

African (AFR) AF: 0.269 AC: 11166 AN: 41442

American (AMR) AF: 0.486 AC: 7371 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1386 AN: 3466

East Asian (EAS) AF: 0.853 AC: 4358 AN: 5112

South Asian (SAS) AF: 0.510 AC: 2450 AN: 4808

European-Finnish (FIN) AF: 0.369 AC: 3886 AN: 10534

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26721 AN: 67816

Other (OTH) AF: 0.380 AC: 800 AN: 2106

Alfa AF: 0.397 Hom.: 51670

Bravo AF: 0.394

Asia WGS AF: 0.641 AC: 2224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.57
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs9363918; hg19: chr6-69142008;