rs1986420

Variant names:

• chr10-117997335-G-A
• rs1986420

Your query was ambiguous. Multiple possible variants found:

• chr10-117997335-G-A
• chr10-117997335-G-C
• chr10-117997335-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 0.692 in 152,134 control chromosomes in the GnomAD database, including 43,219 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 0.69 (43219 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 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: 0.692 AC: 105221 AN: 152016 Hom.: 43226 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.692 AC: 105224 AN: 152134 Hom.: 43219 Cov.: 32 AF XY: 0.686 AC XY: 51006 AN XY: 74370

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.880

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.747

Alfa AF: 0.629 Hom.: 4248

Bravo AF: 0.649

Asia WGS AF: 0.501 AC: 1746 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.4
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1986420; hg19: chr10-119756846;