rs1859972

Variant names:

• chr17-13078982-A-C
• rs1859972

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

ACMG classification

Verdict is Benign. Variant got -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.

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

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

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.305

Alfa AF: 0.335 Hom.: 11522

Bravo AF: 0.295

Asia WGS AF: 0.321 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1859972; hg19: chr17-12982299; COSMIC: COSV53428176;