1-198452278-A-G

Variant names:

• chr1-198452278-A-G
• rs2813164
• ENST00000660823.1:n.805T>C

Variant summary

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

The ENST00000660823.1(ENSG00000287989):​n.805T>C 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 0.533 in 151,840 control chromosomes in the GnomAD database, including 26,074 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 0.53 (26074 hom., cov: 31)
• Consequence: ENSG00000287989 ENST00000660823.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 9 publications found

Genes affected

ENSG00000287989 (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 (EAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371677	XR_922398.3	n.*86T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287989	ENST00000660823.1	n.805T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80788 AN: 151722 Hom.: 26001 Cov.: 31

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.533 AC: 80923 AN: 151840 Hom.: 26074 Cov.: 31 AF XY: 0.543 AC XY: 40335 AN XY: 74220

African (AFR) AF: 0.849 AC: 35188 AN: 41466

American (AMR) AF: 0.598 AC: 9103 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1456 AN: 3460

East Asian (EAS) AF: 0.901 AC: 4652 AN: 5164

South Asian (SAS) AF: 0.703 AC: 3390 AN: 4820

European-Finnish (FIN) AF: 0.399 AC: 4213 AN: 10558

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21567 AN: 67854

Other (OTH) AF: 0.525 AC: 1102 AN: 2100

Alfa AF: 0.393 Hom.: 36351

Bravo AF: 0.561

Asia WGS AF: 0.828 AC: 2871 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.1
DANN	Benign	0.76
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs2813164; hg19: chr1-198421408;