chr1-79983799-G-A

Position:

• chr1-79983799-G-A

Variant summary

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

The ENST00000644002.1(ENSG00000285409):​n.460-15929C>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 0.413 in 151,920 control chromosomes in the GnomAD database, including 13,754 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 0.41 (13754 hom., cov: 32)
• Consequence: ENST00000644002.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 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
	ENST00000644002.1	n.460-15929C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62709 AN: 151802 Hom.: 13753 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.0575

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.413 AC: 62722 AN: 151920 Hom.: 13754 Cov.: 32 AF XY: 0.413 AC XY: 30690 AN XY: 74268

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.0574

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.426

Alfa AF: 0.451 Hom.: 3499

Bravo AF: 0.403

Asia WGS AF: 0.219 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6660164; hg19: chr1-80449484;