chr1-80018321-C-A

Position:

• chr1-80018321-C-A

Variant summary

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

The ENST00000644002.1(ENSG00000285409):​n.459+32225G>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 0.958 in 152,284 control chromosomes in the GnomAD database, including 70,133 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 0.96 (70133 hom., cov: 32)
• Consequence: ENST00000644002.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000644002.1	n.459+32225G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.958 AC: 145843 AN: 152166 Hom.: 70090 Cov.: 32

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.958 AC: 145939 AN: 152284 Hom.: 70133 Cov.: 32 AF XY: 0.955 AC XY: 71150 AN XY: 74468

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.967

Gnomad4 ASJ AF: 0.996

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.982

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.951

Alfa AF: 0.974 Hom.: 18525

Bravo AF: 0.955

Asia WGS AF: 0.832 AC: 2896 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2388956; hg19: chr1-80484006;