rs1869580

Variant names:

• chr1-73865598-C-G
• rs1869580
• ENST00000649962.1:n.271+40331G>C

Variant summary

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

The ENST00000649962.1(ENSG00000285778):​n.271+40331G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 152,136 control chromosomes in the GnomAD database, including 432 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 0.067 (432 hom., cov: 32)
• Consequence: ENSG00000285778 ENST00000649962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759

Genes affected

ENSG00000285778 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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
ENSG00000285778	ENST00000649962.1	n.271+40331G>C		intron_variant	Intron 2 of 3
ENSG00000285778	ENST00000667324.1	n.148+49531G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0668 AC: 10155 AN: 152018 Hom.: 431 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00724

Gnomad FIN AF: 0.0979

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0668 AC: 10167 AN: 152136 Hom.: 432 Cov.: 32 AF XY: 0.0684 AC XY: 5086 AN XY: 74364

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0375

Gnomad4 ASJ AF: 0.0251

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00704

Gnomad4 FIN AF: 0.0979

Gnomad4 NFE AF: 0.0481

Gnomad4 OTH AF: 0.0615

Alfa AF: 0.0612 Hom.: 40

Bravo AF: 0.0646

Asia WGS AF: 0.0160 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.80
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1869580; hg19: chr1-74331281;