chr8-80321732-T-C

Position:

• chr8-80321732-T-C

Variant summary

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

The ENST00000656157.1(ENSG00000253238):​n.273+32730T>C 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 0.871 in 152,230 control chromosomes in the GnomAD database, including 58,271 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 0.87 (58271 hom., cov: 32)
• Consequence: ENST00000656157.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 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+32730T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132440 AN: 152112 Hom.: 58212 Cov.: 32

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.871 AC: 132554 AN: 152230 Hom.: 58271 Cov.: 32 AF XY: 0.867 AC XY: 64503 AN XY: 74426

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.869

Alfa AF: 0.849 Hom.: 23718

Bravo AF: 0.866

Asia WGS AF: 0.697 AC: 2421 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.50
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10090469; hg19: chr8-81233967;