8-80445467-C-T

Position:

• chr8-80445467-C-T

Variant summary

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

The ENST00000656157.1(ENSG00000253238):​n.274-37141C>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 0.448 in 152,072 control chromosomes in the GnomAD database, including 19,739 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 0.45 (19739 hom., cov: 32)
• Consequence: ENST00000656157.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375922	XR_929097.1	n.231-927G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656157.1	n.274-37141C>T		intron_variant, non_coding_transcript_variant
	ENST00000644465.1	n.254-3230C>T		intron_variant, non_coding_transcript_variant
	ENST00000662273.1	n.371-37141C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67967 AN: 151954 Hom.: 19688 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.448 AC: 68067 AN: 152072 Hom.: 19739 Cov.: 32 AF XY: 0.439 AC XY: 32666 AN XY: 74356

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.452

Alfa AF: 0.344 Hom.: 4787

Bravo AF: 0.470

Asia WGS AF: 0.277 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
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: rs400824; hg19: chr8-81357702;