rs41384747

Variant names:

• chr12-7642178-T-G
• rs41384747
• ENST00000642279.1:n.373-4441A>C

Variant summary

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

The ENST00000642279.1(ENSG00000285142):​n.373-4441A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 152,040 control chromosomes in the GnomAD database, including 26,969 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 0.56 (26969 hom., cov: 32)
• Consequence: ENSG00000285142 ENST00000642279.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 2 publications found

Genes affected

ENSG00000285142 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.721 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
ENSG00000285142	ENST00000642279.1	n.373-4441A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85763 AN: 151922 Hom.: 26978 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.564 AC: 85769 AN: 152040 Hom.: 26969 Cov.: 32 AF XY: 0.561 AC XY: 41673 AN XY: 74328

African (AFR) AF: 0.291 AC: 12057 AN: 41468

American (AMR) AF: 0.524 AC: 7994 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2541 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1893 AN: 5170

South Asian (SAS) AF: 0.518 AC: 2496 AN: 4814

European-Finnish (FIN) AF: 0.690 AC: 7290 AN: 10562

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49366 AN: 67972

Other (OTH) AF: 0.612 AC: 1294 AN: 2114

Alfa AF: 0.628 Hom.: 3991

Bravo AF: 0.539

Asia WGS AF: 0.490 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.61
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs41384747; hg19: chr12-7794774;