rs1336433

Positions:

• chr10-111598317-A-C
• chr10-111598317-A-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 0.418 in 151,910 control chromosomes in the GnomAD database, including 13,702 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 0.42 (13702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63515 AN: 151792 Hom.: 13684 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.418 AC: 63559 AN: 151910 Hom.: 13702 Cov.: 32 AF XY: 0.416 AC XY: 30902 AN XY: 74242

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.410

Alfa AF: 0.314 Hom.: 1185

Bravo AF: 0.407

Asia WGS AF: 0.296 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.97
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1336433; hg19: chr10-113358075;