8-24998990-C-T

Position:

• chr8-24998990-C-T

Variant summary

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

The ENST00000522570.1(ENSG00000253832):​n.349+6640C>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 0.0925 in 152,092 control chromosomes in the GnomAD database, including 748 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 0.093 (748 hom., cov: 31)
• Consequence: ENST00000522570.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379330	XR_949591.2	n.474+6640C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522570.1	n.349+6640C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0926 AC: 14073 AN: 151974 Hom.: 750 Cov.: 31

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.0925 AC: 14073 AN: 152092 Hom.: 748 Cov.: 31 AF XY: 0.0921 AC XY: 6850 AN XY: 74366

Gnomad4 AFR AF: 0.0534

Gnomad4 AMR AF: 0.0874

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.0793

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0957

Alfa AF: 0.107 Hom.: 1290

Bravo AF: 0.0855

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17763685; hg19: chr8-24856504;