13-78881697-T-C

Variant names:

• chr13-78881697-T-C
• rs1218282

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.259 AC: 10733 AN: 41452

American (AMR) AF: 0.0573 AC: 876 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0672 AC: 233 AN: 3468

East Asian (EAS) AF: 0.0234 AC: 121 AN: 5182

South Asian (SAS) AF: 0.0471 AC: 227 AN: 4824

European-Finnish (FIN) AF: 0.125 AC: 1330 AN: 10604

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0613 AC: 4170 AN: 68012

Other (OTH) AF: 0.0959 AC: 203 AN: 2116

Alfa AF: 0.0747 Hom.: 2288

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1218282; hg19: chr13-79455832;