rs643009

Variant names:

• chr1-229774990-G-A
• rs643009
• ENST00000775954.1:n.-144G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-229774990-G-A
• chr1-229774990-G-C
• chr1-229774990-G-T

Variant summary

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

The ENST00000775954.1(ENSG00000301071):​n.-144G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 150,232 control chromosomes in the GnomAD database, including 25,193 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 0.57 (25193 hom., cov: 27)
• Consequence: ENSG00000301071 ENST00000775954.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 publications found

Genes affected

ENSG00000301071 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 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
ENSG00000301071	ENST00000775954.1	n.-144G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.570 AC: 85639 AN: 150122 Hom.: 25173 Cov.: 27

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.603

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.570 AC: 85703 AN: 150232 Hom.: 25193 Cov.: 27 AF XY: 0.575 AC XY: 42114 AN XY: 73180

African (AFR) AF: 0.461 AC: 18814 AN: 40774

American (AMR) AF: 0.685 AC: 10286 AN: 15012

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2180 AN: 3460

East Asian (EAS) AF: 0.761 AC: 3840 AN: 5046

South Asian (SAS) AF: 0.665 AC: 3170 AN: 4770

European-Finnish (FIN) AF: 0.576 AC: 5846 AN: 10144

Middle Eastern (MID) AF: 0.604 AC: 174 AN: 288

European-Non Finnish (NFE) AF: 0.588 AC: 39805 AN: 67746

Other (OTH) AF: 0.581 AC: 1211 AN: 2086

Alfa AF: 0.585 Hom.: 84179

Bravo AF: 0.575

Asia WGS AF: 0.676 AC: 2331 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs643009; hg19: chr1-229910737;