rs859665

Variant names:

• chr1-172695302-A-G
• rs859665
• ENST00000725727.1:n.69+24703A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-172695302-A-G
• chr1-172695302-A-T

Variant summary

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

The ENST00000725727.1(ENSG00000224000):​n.69+24703A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,870 control chromosomes in the GnomAD database, including 12,911 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 0.39 (12911 hom., cov: 31)
• Consequence: ENSG00000224000 ENST00000725727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 8 publications found

Genes affected

ENSG00000224000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224000	ENST00000725727.1	n.69+24703A>G		intron_variant	Intron 1 of 1
ENSG00000224000	ENST00000725728.1	n.108+15600A>G		intron_variant	Intron 1 of 1
ENSG00000224000	ENST00000725729.1	n.36+15600A>G		intron_variant	Intron 1 of 2
ENSG00000224000	ENST00000725730.1	n.39+15600A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58837 AN: 151752 Hom.: 12901 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.00889

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.388 AC: 58871 AN: 151870 Hom.: 12911 Cov.: 31 AF XY: 0.380 AC XY: 28209 AN XY: 74256

African (AFR) AF: 0.583 AC: 24155 AN: 41412

American (AMR) AF: 0.310 AC: 4722 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1233 AN: 3470

East Asian (EAS) AF: 0.00891 AC: 46 AN: 5160

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4818

European-Finnish (FIN) AF: 0.303 AC: 3203 AN: 10566

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23134 AN: 67900

Other (OTH) AF: 0.358 AC: 755 AN: 2108

Alfa AF: 0.326 Hom.: 5316

Bravo AF: 0.399

Asia WGS AF: 0.151 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.55
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs859665; hg19: chr1-172664442; COSMIC: COSV56922091;