rs10506678

Variant names:

• chr12-75028425-G-T
• rs10506678
• ENST00000547040.1:n.218+2221G>T

Variant summary

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

The ENST00000547040.1(ENSG00000257434):​n.218+2221G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,966 control chromosomes in the GnomAD database, including 17,091 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 0.44 (17091 hom., cov: 31)
• Consequence: ENSG00000257434 ENST00000547040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

Genes affected

ENSG00000257434 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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
ENSG00000257434	ENST00000547040.1	n.218+2221G>T		intron_variant	Intron 1 of 1	2
ENSG00000257434	ENST00000549762.1	n.228+3240G>T		intron_variant	Intron 2 of 2	3
ENSG00000257434	ENST00000550049.1	n.231+2221G>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67157 AN: 151848 Hom.: 17082 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.442 AC: 67184 AN: 151966 Hom.: 17091 Cov.: 31 AF XY: 0.440 AC XY: 32676 AN XY: 74258

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.459

Alfa AF: 0.544 Hom.: 48611

Bravo AF: 0.421

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.078
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506678; hg19: chr12-75422205;