ENST00000690652.3:n.356-10268G>A

Variant names:

• chr6-23467938-C-T
• rs10484538
• ENST00000690652.3:n.356-10268G>A

Variant summary

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

The ENST00000690652.3(ENSG00000289368):​n.356-10268G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 152,008 control chromosomes in the GnomAD database, including 183 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 0.034 (183 hom., cov: 31)
• Consequence: ENSG00000289368 ENST00000690652.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 2 publications found

Genes affected

ENSG00000289368 (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 (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374976	XR_001744046.2	n.401-10268G>A		intron_variant	Intron 3 of 6
LOC105374976	XR_007059501.1	n.379-10268G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289368	ENST00000690652.3	n.356-10268G>A		intron_variant	Intron 1 of 2
ENSG00000289368	ENST00000700866.2	n.181-10268G>A		intron_variant	Intron 1 of 2
ENSG00000289368	ENST00000702216.2	n.203-10268G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0341 AC: 5186 AN: 151890 Hom.: 181 Cov.: 31

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0189

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0342 AC: 5197 AN: 152008 Hom.: 183 Cov.: 31 AF XY: 0.0364 AC XY: 2704 AN XY: 74288

African (AFR) AF: 0.0390 AC: 1620 AN: 41498

American (AMR) AF: 0.0189 AC: 287 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3466

East Asian (EAS) AF: 0.207 AC: 1066 AN: 5140

South Asian (SAS) AF: 0.0956 AC: 461 AN: 4820

European-Finnish (FIN) AF: 0.0268 AC: 284 AN: 10606

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0178 AC: 1206 AN: 67942

Other (OTH) AF: 0.0318 AC: 67 AN: 2110

Alfa AF: 0.00988 Hom.: 2

Bravo AF: 0.0343

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0070
DANN	Benign	0.66
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10484538; hg19: chr6-23468166;