rs10500968

chr11-23801921-T-Cchr11-23801921-T-G

Variant summary

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

The ENST00000525512.2(ENSG00000254861):n.264+2558A>G 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 0.0768 in 152,250 control chromosomes in the GnomAD database, including 1,097 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 0.077 (1097 hom., cov: 32)
• Consequence: ENST00000525512.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000525512.2	n.264+2558A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0768 AC: 11677 AN: 152130 Hom.: 1096 Cov.: 32

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.0760

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

GnomAD4 genome AF: 0.0768 AC: 11689 AN: 152250 Hom.: 1097 Cov.: 32 AF XY: 0.0812 AC XY: 6044 AN XY: 74434

Gnomad4 AFR AF: 0.0166

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.0236

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.0645

Gnomad4 OTH AF: 0.0795

Alfa AF: 0.0645 Hom.: 256

Bravo AF: 0.0867

Asia WGS AF: 0.301 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.50
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500968; hg19: chr11-23823467;