rs1819003

Variant names:

• chr2-77978776-A-G
• rs1819003
• ENST00000667782.1:n.83-38890T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-77978776-A-G
• chr2-77978776-A-T

Variant summary

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

The ENST00000667782.1(ENSG00000227088):​n.83-38890T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.858 in 151,264 control chromosomes in the GnomAD database, including 55,756 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 (55756 hom., cov: 26)
• Consequence: ENSG00000227088 ENST00000667782.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 0 publications found

Genes affected

ENSG00000227088 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927967	NR_110288.1	n.345-103714T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227088	ENST00000667782.1	n.83-38890T>C		intron_variant	Intron 1 of 6
ENSG00000227088	ENST00000759916.1	n.269+19302T>C		intron_variant	Intron 3 of 4
ENSG00000227088	ENST00000759917.1	n.267+19302T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.858 AC: 129615 AN: 151150 Hom.: 55709 Cov.: 26

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.858 AC: 129719 AN: 151264 Hom.: 55756 Cov.: 26 AF XY: 0.862 AC XY: 63611 AN XY: 73832

African (AFR) AF: 0.914 AC: 37707 AN: 41236

American (AMR) AF: 0.848 AC: 12881 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2927 AN: 3466

East Asian (EAS) AF: 0.900 AC: 4537 AN: 5040

South Asian (SAS) AF: 0.905 AC: 4322 AN: 4776

European-Finnish (FIN) AF: 0.868 AC: 9029 AN: 10404

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55502 AN: 67844

Other (OTH) AF: 0.866 AC: 1816 AN: 2096

Alfa AF: 0.835 Hom.: 6196

Bravo AF: 0.858

Asia WGS AF: 0.922 AC: 3206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1819003; hg19: chr2-78205902;