chr1-78300696-C-A

Variant names:

• chr1-78300696-C-A
• rs720887
• ENST00000413519.1:n.683-41830C>A

Variant summary

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

The ENST00000413519.1(MGC27382):​n.683-41830C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,922 control chromosomes in the GnomAD database, including 21,115 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 0.52 (21115 hom., cov: 31)
• Consequence: MGC27382 ENST00000413519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802
• Publications: 3 publications found

Genes affected

MGC27382 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGC27382	NR_027310.2	n.706-41830C>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGC27382	ENST00000413519.1	n.683-41830C>A		intron_variant	Intron 3 of 5	2

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78775 AN: 151804 Hom.: 21116 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.519 AC: 78799 AN: 151922 Hom.: 21115 Cov.: 31 AF XY: 0.523 AC XY: 38802 AN XY: 74260

African (AFR) AF: 0.403 AC: 16693 AN: 41426

American (AMR) AF: 0.460 AC: 7016 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3468

East Asian (EAS) AF: 0.752 AC: 3883 AN: 5162

South Asian (SAS) AF: 0.584 AC: 2807 AN: 4804

European-Finnish (FIN) AF: 0.625 AC: 6592 AN: 10540

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37867 AN: 67944

Other (OTH) AF: 0.524 AC: 1108 AN: 2114

Alfa AF: 0.539 Hom.: 71395

Bravo AF: 0.500

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.40
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs720887; hg19: chr1-78766380;