rs10500600

chr11-4419253-G-Achr11-4419253-G-T

Variant summary

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

The ENST00000690302.1(ENSG00000291144):n.379+25088G>A 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 0.0613 in 152,100 control chromosomes in the GnomAD database, including 356 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 0.061 (356 hom., cov: 32)
• Consequence: ENST00000690302.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.107 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
	ENST00000690302.1	n.379+25088G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0613 AC: 9313 AN: 151982 Hom.: 352 Cov.: 32

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0562

Gnomad FIN AF: 0.0448

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0613 AC: 9331 AN: 152100 Hom.: 356 Cov.: 32 AF XY: 0.0606 AC XY: 4501 AN XY: 74322

Gnomad4 AFR AF: 0.0519

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0594

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0561

Gnomad4 FIN AF: 0.0448

Gnomad4 NFE AF: 0.0645

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0610 Hom.: 477

Bravo AF: 0.0661

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	8.2
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500600; hg19: chr11-4440483;