8-101451374-G-A

Position:

• chr8-101451374-G-A

Variant summary

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

The ENST00000519793.1(ENSG00000254084):​n.242+837C>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 0.672 in 151,992 control chromosomes in the GnomAD database, including 35,091 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 0.67 (35091 hom., cov: 32)
• Consequence: ENST00000519793.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000519793.1	n.242+837C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102108 AN: 151874 Hom.: 35088 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.672 AC: 102143 AN: 151992 Hom.: 35091 Cov.: 32 AF XY: 0.671 AC XY: 49863 AN XY: 74304

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.677

Alfa AF: 0.653 Hom.: 5642

Bravo AF: 0.652

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs678347; hg19: chr8-102463602;