8-31295637-T-C

Position:

• chr8-31295637-T-C

Variant summary

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

The ENST00000670110.1(ENSG00000253377):​n.194+19829T>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 0.568 in 151,758 control chromosomes in the GnomAD database, including 24,717 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 0.57 (24717 hom., cov: 30)
• Consequence: ENST00000670110.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929492	XR_949649.3	n.1018+19829T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670110.1	n.194+19829T>C		intron_variant, non_coding_transcript_variant
	ENST00000524022.1	n.213+19829T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000655813.1	n.267+19829T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86185 AN: 151644 Hom.: 24708 Cov.: 30

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.568 AC: 86236 AN: 151758 Hom.: 24717 Cov.: 30 AF XY: 0.569 AC XY: 42159 AN XY: 74138

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.570

Alfa AF: 0.563 Hom.: 11029

Bravo AF: 0.571

Asia WGS AF: 0.693 AC: 2409 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	0.82
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4634594; hg19: chr8-31153153;