rs10504306

chr8-60063612-C-T

Variant summary

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

The ENST00000655977.1(ENSG00000254775):n.231-10982C>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 0.0371 in 152,048 control chromosomes in the GnomAD database, including 292 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 0.037 (292 hom., cov: 32)
• Consequence: ENST00000655977.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375861	XR_001745714.3	n.502+5084C>T		intron_variant, non_coding_transcript_variant
LOC105375861	XR_002956710.2	n.502+5084C>T		intron_variant, non_coding_transcript_variant
LOC105375861	XR_007060918.1	n.225-10982C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000655977.1	n.231-10982C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0371 AC: 5643 AN: 151930 Hom.: 291 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0259

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.00462

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00185

Gnomad OTH AF: 0.0307

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

GnomAD4 genome AF: 0.0371 AC: 5642 AN: 152048 Hom.: 292 Cov.: 32 AF XY: 0.0377 AC XY: 2799 AN XY: 74332

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.0259

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0232

Gnomad4 FIN AF: 0.00462

Gnomad4 NFE AF: 0.00185

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.0251 Hom.: 36

Bravo AF: 0.0422

Asia WGS AF: 0.0650 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504306; hg19: chr8-60976171;