8-34187743-C-T

Variant names:

• chr8-34187743-C-T
• rs9297216
• ENST00000518217.2:n.868+2838C>T

Variant summary

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

The ENST00000518217.2(ENSG00000254302):​n.868+2838C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,054 control chromosomes in the GnomAD database, including 2,406 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 0.17 (2406 hom., cov: 32)
• Consequence: ENSG00000254302 ENST00000518217.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 6 publications found

Genes affected

ENSG00000254302 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379364	NR_189605.1	n.1651+2838C>T		intron_variant	Intron 8 of 11
LOC105379364	NR_189606.1	n.1243+2838C>T		intron_variant	Intron 7 of 9
LOC105379364	NR_189607.1	n.1197+2838C>T		intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254302	ENST00000518217.2	n.868+2838C>T		intron_variant	Intron 4 of 4	3
ENSG00000254302	ENST00000671048.1	n.261+2838C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26035 AN: 151934 Hom.: 2404 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.171 AC: 26050 AN: 152054 Hom.: 2406 Cov.: 32 AF XY: 0.175 AC XY: 13003 AN XY: 74320

African (AFR) AF: 0.194 AC: 8069 AN: 41486

American (AMR) AF: 0.201 AC: 3069 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1493 AN: 5152

South Asian (SAS) AF: 0.281 AC: 1350 AN: 4812

European-Finnish (FIN) AF: 0.160 AC: 1687 AN: 10576

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9583 AN: 67970

Other (OTH) AF: 0.165 AC: 349 AN: 2110

Alfa AF: 0.125 Hom.: 394

Bravo AF: 0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.44
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs9297216; hg19: chr8-34045261;