rs1998591

Positions:

• chr10-94648221-G-A

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 0.278 in 152,114 control chromosomes in the GnomAD database, including 6,445 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 0.28 (6445 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.94648221G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42209 AN: 151996 Hom.: 6434 Cov.: 33

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.278 AC: 42251 AN: 152114 Hom.: 6445 Cov.: 33 AF XY: 0.281 AC XY: 20912 AN XY: 74364

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.256

Alfa AF: 0.232 Hom.: 8621

Bravo AF: 0.274

Asia WGS AF: 0.443 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1998591; hg19: chr10-96407978;