rs9959310

Variant names:

• chr18-62414634-T-C
• rs9959310

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 0.197 in 152,180 control chromosomes in the GnomAD database, including 3,226 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 0.20 (3226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.231 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: 0.197 AC: 29964 AN: 152062 Hom.: 3228 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.197 AC: 29973 AN: 152180 Hom.: 3226 Cov.: 32 AF XY: 0.193 AC XY: 14368 AN XY: 74420

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.0231

Gnomad4 SAS AF: 0.0562

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.196

Alfa AF: 0.207 Hom.: 1464

Bravo AF: 0.200

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.1
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9959310; hg19: chr18-60081867;