chr1-115280766-G-A

Position:

• chr1-115280766-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649888.1(ENSG00000285698):​n.214+2784C>T 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 0.461 in 152,054 control chromosomes in the GnomAD database, including 17,271 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 0.46 (17271 hom., cov: 32)
• Consequence: ENST00000649888.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000649888.1	n.214+2784C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69961 AN: 151938 Hom.: 17240 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.461 AC: 70038 AN: 152054 Hom.: 17271 Cov.: 32 AF XY: 0.462 AC XY: 34342 AN XY: 74306

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.450

Alfa AF: 0.402 Hom.: 17250

Bravo AF: 0.477

Asia WGS AF: 0.538 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7523086; hg19: chr1-115823387;