1-207495285-C-T

Variant names:

• chr1-207495285-C-T
• rs9429942
• ENST00000809561.1:n.512G>A

Variant summary

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

The ENST00000809561.1(ENSG00000305204):​n.512G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,260 control chromosomes in the GnomAD database, including 32,344 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 0.64 (32344 hom., cov: 28)
• Consequence: ENSG00000305204 ENST00000809561.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 11 publications found

Genes affected

ENSG00000305204 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305204	ENST00000809561.1	n.512G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000305204	ENST00000809562.1	n.585G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97333 AN: 151140 Hom.: 32345 Cov.: 28

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.689

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.644 AC: 97352 AN: 151260 Hom.: 32344 Cov.: 28 AF XY: 0.652 AC XY: 48155 AN XY: 73892

African (AFR) AF: 0.481 AC: 19713 AN: 40990

American (AMR) AF: 0.723 AC: 11018 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2375 AN: 3470

East Asian (EAS) AF: 0.958 AC: 4947 AN: 5162

South Asian (SAS) AF: 0.825 AC: 3953 AN: 4794

European-Finnish (FIN) AF: 0.718 AC: 7511 AN: 10456

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.673 AC: 45663 AN: 67856

Other (OTH) AF: 0.652 AC: 1365 AN: 2092

Alfa AF: 0.642 Hom.: 3794

Bravo AF: 0.640

Asia WGS AF: 0.858 AC: 2981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.67
DANN	Benign	0.86
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs9429942; hg19: chr1-207668630;