rs10506339

Variant names:

• chr12-55036618-A-G
• rs10506339
• ENST00000781897.1:n.93-7298T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000781897.1(ENSG00000301788):​n.93-7298T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0614 in 152,148 control chromosomes in the GnomAD database, including 724 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 (724 hom., cov: 32)
• Consequence: ENSG00000301788 ENST00000781897.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 3 publications found

Genes affected

ENSG00000301788 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301788	ENST00000781897.1	n.93-7298T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0614 AC: 9331 AN: 152030 Hom.: 725 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0403

Gnomad ASJ AF: 0.0586

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.0594

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

GnomAD4 genome AF: 0.0614 AC: 9343 AN: 152148 Hom.: 724 Cov.: 32 AF XY: 0.0591 AC XY: 4399 AN XY: 74394

African (AFR) AF: 0.181 AC: 7497 AN: 41482

American (AMR) AF: 0.0402 AC: 615 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0586 AC: 203 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4828

European-Finnish (FIN) AF: 0.0000943 AC: 1 AN: 10606

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.0121 AC: 826 AN: 67988

Other (OTH) AF: 0.0588 AC: 124 AN: 2110

Alfa AF: 0.0295 Hom.: 962

Bravo AF: 0.0699

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.36
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10506339; hg19: chr12-55430402;