rs10798004

Variant names:

• chr1-185296017-G-A
• rs10798004

Your query was ambiguous. Multiple possible variants found:

• chr1-185296017-G-A
• chr1-185296017-G-C
• chr1-185296017-G-T

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 0.519 in 151,504 control chromosomes in the GnomAD database, including 21,824 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 0.52 (21824 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

ACMG classification

Verdict is Benign. Variant got -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 = 0.725 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: 0.519 AC: 78558 AN: 151398 Hom.: 21790 Cov.: 30

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.519 AC: 78645 AN: 151504 Hom.: 21824 Cov.: 30 AF XY: 0.518 AC XY: 38282 AN XY: 73970

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.467

Alfa AF: 0.447 Hom.: 24592

Bravo AF: 0.524

Asia WGS AF: 0.437 AC: 1515 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10798004; hg19: chr1-185265149;