1-78296512-T-G

Variant names:

• chr1-78296512-T-G
• rs12134625
• ENST00000413519.1:n.682+44635T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000413519.1(MGC27382):​n.682+44635T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,052 control chromosomes in the GnomAD database, including 16,686 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 0.45 (16686 hom., cov: 33)
• Consequence: MGC27382 ENST00000413519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.79
• Publications: 1 publications found

Genes affected

MGC27382 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGC27382	NR_027310.2	n.705+44635T>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGC27382	ENST00000413519.1	n.682+44635T>G		intron_variant	Intron 3 of 5	2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67984 AN: 151934 Hom.: 16695 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.447 AC: 67978 AN: 152052 Hom.: 16686 Cov.: 33 AF XY: 0.443 AC XY: 32918 AN XY: 74356

African (AFR) AF: 0.261 AC: 10832 AN: 41494

American (AMR) AF: 0.476 AC: 7270 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1967 AN: 3466

East Asian (EAS) AF: 0.207 AC: 1070 AN: 5172

South Asian (SAS) AF: 0.480 AC: 2313 AN: 4820

European-Finnish (FIN) AF: 0.468 AC: 4952 AN: 10570

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.561 AC: 38097 AN: 67942

Other (OTH) AF: 0.451 AC: 953 AN: 2112

Alfa AF: 0.376 Hom.: 1389

Bravo AF: 0.441

Asia WGS AF: 0.324 AC: 1124 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	15
DANN	Benign	0.92
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs12134625; hg19: chr1-78762196;