rs1218282

chr13-78881697-T-C

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 0.118 in 152,152 control chromosomes in the GnomAD database, including 1,695 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 0.12 (1695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17919 AN: 152034 Hom.: 1684 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0574

Gnomad ASJ AF: 0.0672

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.0481

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0613

Gnomad OTH AF: 0.0974

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

GnomAD4 genome AF: 0.118 AC: 17964 AN: 152152 Hom.: 1695 Cov.: 32 AF XY: 0.116 AC XY: 8641 AN XY: 74412

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.0573

Gnomad4 ASJ AF: 0.0672

Gnomad4 EAS AF: 0.0234

Gnomad4 SAS AF: 0.0471

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0613

Gnomad4 OTH AF: 0.0959

Alfa AF: 0.0622 Hom.: 507

Bravo AF: 0.118

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.047
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1218282; hg19: chr13-79455832;