rs985000

Variant names:

• chr10-22313047-G-A
• rs985000

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 0.0449 in 152,218 control chromosomes in the GnomAD database, including 194 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 0.045 (194 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

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 = 0.0654 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: 0.0449 AC: 6833 AN: 152100 Hom.: 194 Cov.: 33

Gnomad AFR AF: 0.0148

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0689

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0267

Gnomad FIN AF: 0.0617

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0605

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0449 AC: 6834 AN: 152218 Hom.: 194 Cov.: 33 AF XY: 0.0442 AC XY: 3289 AN XY: 74402

Gnomad4 AFR AF: 0.0148

Gnomad4 AMR AF: 0.0689

Gnomad4 ASJ AF: 0.0427

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0267

Gnomad4 FIN AF: 0.0617

Gnomad4 NFE AF: 0.0605

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.0566 Hom.: 345

Bravo AF: 0.0456

Asia WGS AF: 0.0110 AC: 39 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	0.81
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs985000; hg19: chr10-22601976;