rs10506678

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000257434 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.186 AC: 7725 AN: 41464

American (AMR) AF: 0.444 AC: 6783 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3466

East Asian (EAS) AF: 0.382 AC: 1968 AN: 5156

South Asian (SAS) AF: 0.364 AC: 1751 AN: 4810

European-Finnish (FIN) AF: 0.602 AC: 6350 AN: 10550

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39596 AN: 67948

Other (OTH) AF: 0.459 AC: 966 AN: 2106

Alfa AF: 0.529 Hom.: 99224

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10506678; hg19: chr12-75422205;