8-38616966-C-T

Variant names:

• chr8-38616966-C-T
• rs1000236
• ENST00000693585.2:n.329-1330C>T

Variant summary

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

The ENST00000693585.2(ENSG00000289104):​n.329-1330C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,020 control chromosomes in the GnomAD database, including 12,000 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 0.38 (12000 hom., cov: 32)
• Consequence: ENSG00000289104 ENST00000693585.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 4 publications found

Genes affected

ENSG00000289104 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000693585.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289104	ENST00000693585.2		n.329-1330C>T		intron	N/A
	ENSG00000296158	ENST00000736924.1		n.100-13980G>A		intron	N/A
	ENSG00000289104	ENST00000737070.1		n.387+481C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57259 AN: 151902 Hom.: 11991 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.377 AC: 57283 AN: 152020 Hom.: 12000 Cov.: 32 AF XY: 0.381 AC XY: 28338 AN XY: 74288

African (AFR) AF: 0.178 AC: 7368 AN: 41448

American (AMR) AF: 0.501 AC: 7660 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1630 AN: 3470

East Asian (EAS) AF: 0.385 AC: 1987 AN: 5160

South Asian (SAS) AF: 0.434 AC: 2091 AN: 4814

European-Finnish (FIN) AF: 0.440 AC: 4651 AN: 10560

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30521 AN: 67966

Other (OTH) AF: 0.402 AC: 850 AN: 2112

Alfa AF: 0.424 Hom.: 42691

Bravo AF: 0.375

Asia WGS AF: 0.363 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1000236; hg19: chr8-38474484;