rs1859972

Variant names:

• chr17-13078982-A-C
• rs1859972
• ENST00000808889.1:n.921-21332A>C

Your query was ambiguous. Multiple possible variants found:

• chr17-13078982-A-C
• chr17-13078982-A-G

Variant summary

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

The ENST00000808889.1(ENSG00000273098):​n.921-21332A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,134 control chromosomes in the GnomAD database, including 7,619 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 0.30 (7619 hom., cov: 32)
• Consequence: ENSG00000273098 ENST00000808889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 6 publications found

Genes affected

ENSG00000273098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808889.1. 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
	ENSG00000273098	ENST00000808889.1		n.921-21332A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45667 AN: 152016 Hom.: 7618 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.300 AC: 45676 AN: 152134 Hom.: 7619 Cov.: 32 AF XY: 0.308 AC XY: 22873 AN XY: 74378

African (AFR) AF: 0.155 AC: 6426 AN: 41518

American (AMR) AF: 0.416 AC: 6361 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 865 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1538 AN: 5160

South Asian (SAS) AF: 0.327 AC: 1580 AN: 4830

European-Finnish (FIN) AF: 0.399 AC: 4220 AN: 10568

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.347 AC: 23590 AN: 67976

Other (OTH) AF: 0.305 AC: 646 AN: 2116

Alfa AF: 0.330 Hom.: 14366

Bravo AF: 0.295

Asia WGS AF: 0.321 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.43
PhyloP100		-0.22

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: rs1859972;

hg19: chr17-12982299;

COSMIC: COSV53428176;