rs10506466

chr12-63755759-A-G

Variant summary

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

The ENST00000509615.2(ENSG00000249753):n.238+39722T>C 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 0.117 in 152,154 control chromosomes in the GnomAD database, including 1,371 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 0.12 (1371 hom., cov: 32)
• Consequence: ENST00000509615.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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
	ENST00000509615.2	n.238+39722T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17707 AN: 152036 Hom.: 1367 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0802

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0826

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.117 AC: 17733 AN: 152154 Hom.: 1371 Cov.: 32 AF XY: 0.117 AC XY: 8708 AN XY: 74390

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0802

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0826

Gnomad4 NFE AF: 0.0756

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0881 Hom.: 132

Bravo AF: 0.123

Asia WGS AF: 0.265 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.24
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506466; hg19: chr12-64149539;