rs2807845

Variant names:

• chr1-220822945-G-T
• rs2807845
• ENST00000651706.1:n.842+17671G>T

Variant summary

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

The ENST00000651706.1(ENSG00000286231):​n.842+17671G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,998 control chromosomes in the GnomAD database, including 16,976 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 0.47 (16976 hom., cov: 32)
• Consequence: ENSG00000286231 ENST00000651706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 4 publications found

Genes affected

ENSG00000286231 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651706.1. 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
	ENSG00000286231	ENST00000651706.1		n.842+17671G>T		intron	N/A	ENSP00000499157.1	A0A494C1P3

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71602 AN: 151880 Hom.: 16945 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.472 AC: 71679 AN: 151998 Hom.: 16976 Cov.: 32 AF XY: 0.471 AC XY: 35029 AN XY: 74296

African (AFR) AF: 0.520 AC: 21526 AN: 41430

American (AMR) AF: 0.456 AC: 6959 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3470

East Asian (EAS) AF: 0.481 AC: 2488 AN: 5168

South Asian (SAS) AF: 0.422 AC: 2028 AN: 4810

European-Finnish (FIN) AF: 0.472 AC: 4973 AN: 10542

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30716 AN: 67988

Other (OTH) AF: 0.455 AC: 960 AN: 2112

Alfa AF: 0.467 Hom.: 2372

Bravo AF: 0.475

Asia WGS AF: 0.454 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.026
DANN	Benign	0.29
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2807845; hg19: chr1-220996287;