1-78296512-T-G

Position:

• chr1-78296512-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_027310.2(MGC27382):​n.705+44635T>G variant causes a intron, non coding transcript 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 NR_027310.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.79

Genes affected

MGC27382 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MGC27382	NR_027310.2	n.705+44635T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGC27382	ENST00000413519.1	n.682+44635T>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.451

Alfa AF: 0.382 Hom.: 1360

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12134625; hg19: chr1-78762196;