rs2070803

Variant names:

• chr1-155185239-G-A
• rs2070803
• ENST00000473363.3:c.48+1986C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-155185239-G-A
• chr1-155185239-G-C
• chr1-155185239-G-T

Variant summary

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

The ENST00000473363.3(ENSG00000273088):​c.48+1986C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,112 control chromosomes in the GnomAD database, including 23,407 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 0.55 (23407 hom., cov: 34)
• Consequence: ENSG00000273088 ENST00000473363.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 38 publications found

Genes affected

ENSG00000273088 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000473363.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000273088	ENST00000473363.3	TSL:5	c.48+1986C>T		intron	N/A	ENSP00000477381.3	V9GZ38

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83511 AN: 151994 Hom.: 23378 Cov.: 34

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.549 AC: 83584 AN: 152112 Hom.: 23407 Cov.: 34 AF XY: 0.543 AC XY: 40406 AN XY: 74360

African (AFR) AF: 0.584 AC: 24218 AN: 41488

American (AMR) AF: 0.451 AC: 6902 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2115 AN: 3470

East Asian (EAS) AF: 0.246 AC: 1271 AN: 5166

South Asian (SAS) AF: 0.537 AC: 2591 AN: 4822

European-Finnish (FIN) AF: 0.492 AC: 5207 AN: 10578

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39322 AN: 67982

Other (OTH) AF: 0.551 AC: 1162 AN: 2110

Alfa AF: 0.575 Hom.: 5037

Bravo AF: 0.542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
PhyloP100		0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2070803;

hg19: chr1-155157715;