8-80378152-C-T

Position:

• chr8-80378152-C-T

Variant summary

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

The ENST00000656157.1(ENSG00000253238):​n.273+89150C>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 0.505 in 151,746 control chromosomes in the GnomAD database, including 21,187 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 0.51 (21187 hom., cov: 29)
• Consequence: ENST00000656157.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 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
	ENST00000656157.1	n.273+89150C>T		intron_variant, non_coding_transcript_variant
	ENST00000644465.1	n.254-70545C>T		intron_variant, non_coding_transcript_variant
	ENST00000656811.1	n.252-24584C>T		intron_variant, non_coding_transcript_variant
	ENST00000662273.1	n.370+89150C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76646 AN: 151628 Hom.: 21193 Cov.: 29

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.505 AC: 76641 AN: 151746 Hom.: 21187 Cov.: 29 AF XY: 0.508 AC XY: 37660 AN XY: 74162

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.525

Alfa AF: 0.445 Hom.: 1496

Bravo AF: 0.480

Asia WGS AF: 0.495 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2370615; hg19: chr8-81290387;