rs10512948

chr5-8233238-T-C

Variant summary

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

The ENST00000654773.1(ENSG00000288002):n.262-23394A>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 0.159 in 152,208 control chromosomes in the GnomAD database, including 2,373 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 0.16 (2373 hom., cov: 33)
• Consequence: ENST00000654773.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675

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 = 0.393 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
	ENST00000654773.1	n.262-23394A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24217 AN: 152090 Hom.: 2364 Cov.: 33

Gnomad AFR AF: 0.0983

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.159 AC: 24238 AN: 152208 Hom.: 2373 Cov.: 33 AF XY: 0.166 AC XY: 12322 AN XY: 74406

Gnomad4 AFR AF: 0.0983

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.197

Alfa AF: 0.159 Hom.: 3949

Bravo AF: 0.160

Asia WGS AF: 0.344 AC: 1195 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	2.2
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512948; hg19: chr5-8233351;