rs34886602

Variant names:

• chr18-57590297-C-T
• rs34886602

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 0.0787 in 152,110 control chromosomes in the GnomAD database, including 937 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 0.079 (937 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 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: 0.0787 AC: 11961 AN: 151988 Hom.: 932 Cov.: 33

Gnomad AFR AF: 0.0223

Gnomad AMI AF: 0.00991

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0611

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.0787 AC: 11978 AN: 152110 Hom.: 937 Cov.: 33 AF XY: 0.0864 AC XY: 6424 AN XY: 74340

African (AFR) AF: 0.0223 AC: 925 AN: 41526

American (AMR) AF: 0.194 AC: 2958 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1712 AN: 5150

South Asian (SAS) AF: 0.0989 AC: 477 AN: 4824

European-Finnish (FIN) AF: 0.132 AC: 1398 AN: 10554

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0611 AC: 4156 AN: 67998

Other (OTH) AF: 0.0740 AC: 156 AN: 2108

Alfa AF: 0.0713 Hom.: 82

Bravo AF: 0.0850

Asia WGS AF: 0.199 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.74
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs34886602; hg19: chr18-55257529;