8-34187743-C-T

Position:

• chr8-34187743-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000671048.1(ENSG00000254302):​n.261+2838C>T variant causes a intron, non coding transcript 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: ENST00000671048.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105379365	XR_949660.2	n.618+2838C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000671048.1	n.261+2838C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0986

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.165

Alfa AF: 0.119 Hom.: 326

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9297216; hg19: chr8-34045261;