rs990707

Variant names:

• chr1-175809837-G-C
• rs990707
• ENST00000775782.1:n.373-65G>C

Variant summary

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

The ENST00000775782.1(ENSG00000301049):​n.373-65G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 152,180 control chromosomes in the GnomAD database, including 56,019 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 0.86 (56019 hom., cov: 32)
• Consequence: ENSG00000301049 ENST00000775782.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 0 publications found

Genes affected

ENSG00000301049 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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
ENSG00000301049	ENST00000775782.1	n.373-65G>C		intron_variant	Intron 2 of 2
ENSG00000301049	ENST00000775783.1	n.317-65G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130347 AN: 152062 Hom.: 55992 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.857 AC: 130423 AN: 152180 Hom.: 56019 Cov.: 32 AF XY: 0.856 AC XY: 63677 AN XY: 74382

African (AFR) AF: 0.887 AC: 36835 AN: 41510

American (AMR) AF: 0.830 AC: 12685 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3076 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4872 AN: 5182

South Asian (SAS) AF: 0.834 AC: 4014 AN: 4812

European-Finnish (FIN) AF: 0.814 AC: 8612 AN: 10582

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57406 AN: 68010

Other (OTH) AF: 0.872 AC: 1843 AN: 2114

Alfa AF: 0.849 Hom.: 6816

Bravo AF: 0.856

Asia WGS AF: 0.869 AC: 3019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.53
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs990707; hg19: chr1-175778973; COSMIC: COSV107160078;