rs1299348

Variant names:

• chr18-13822257-T-C
• rs1299348

Your query was ambiguous. Multiple possible variants found:

• chr18-13822257-T-C
• chr18-13822257-T-G

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 0.428 in 152,092 control chromosomes in the GnomAD database, including 15,579 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 0.43 (15579 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 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: 0.428 AC: 64992 AN: 151974 Hom.: 15546 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.428 AC: 65080 AN: 152092 Hom.: 15579 Cov.: 32 AF XY: 0.424 AC XY: 31531 AN XY: 74364

African (AFR) AF: 0.658 AC: 27309 AN: 41490

American (AMR) AF: 0.400 AC: 6115 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1030 AN: 3462

East Asian (EAS) AF: 0.428 AC: 2208 AN: 5156

South Asian (SAS) AF: 0.282 AC: 1362 AN: 4824

European-Finnish (FIN) AF: 0.312 AC: 3300 AN: 10582

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22574 AN: 67968

Other (OTH) AF: 0.394 AC: 832 AN: 2114

Alfa AF: 0.366 Hom.: 23947

Bravo AF: 0.445

Asia WGS AF: 0.359 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.017
DANN	Benign	0.38
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1299348; hg19: chr18-13822256;