rs1810636

Variant names:

• chr20-2674279-A-C
• rs1810636
• ENST00000814883.1:n.155-3839T>G

Your query was ambiguous. Multiple possible variants found:

• chr20-2674279-A-C
• chr20-2674279-A-G
• chr20-2674279-A-T

Variant summary

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

The ENST00000814883.1(ENSG00000306031):​n.155-3839T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,632 control chromosomes in the GnomAD database, including 32,588 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 0.65 (32588 hom., cov: 31)
• Consequence: ENSG00000306031 ENST00000814883.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 19 publications found

Genes affected

ENSG00000306031 (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 = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372507	XR_937210.3	n.681-3839T>G		intron_variant	Intron 2 of 2
LOC105372507	XR_937211.3	n.681-3696T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306031	ENST00000814883.1	n.155-3839T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99020 AN: 151512 Hom.: 32539 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.635

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.654 AC: 99132 AN: 151632 Hom.: 32588 Cov.: 31 AF XY: 0.654 AC XY: 48495 AN XY: 74098

African (AFR) AF: 0.698 AC: 28826 AN: 41310

American (AMR) AF: 0.686 AC: 10465 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2003 AN: 3468

East Asian (EAS) AF: 0.487 AC: 2474 AN: 5084

South Asian (SAS) AF: 0.605 AC: 2906 AN: 4800

European-Finnish (FIN) AF: 0.669 AC: 7047 AN: 10540

Middle Eastern (MID) AF: 0.639 AC: 184 AN: 288

European-Non Finnish (NFE) AF: 0.639 AC: 43370 AN: 67880

Other (OTH) AF: 0.646 AC: 1353 AN: 2096

Alfa AF: 0.628 Hom.: 65869

Bravo AF: 0.653

Asia WGS AF: 0.582 AC: 2028 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	1.5
DANN	Benign	0.48
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1810636; hg19: chr20-2654925;