rs955427

Positions:

• chr18-61222840-T-C
• chr18-61222840-T-G

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 0.596 in 151,914 control chromosomes in the GnomAD database, including 28,635 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 0.60 (28635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.713 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: 0.597 AC: 90548 AN: 151794 Hom.: 28623 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.596 AC: 90588 AN: 151914 Hom.: 28635 Cov.: 32 AF XY: 0.592 AC XY: 43952 AN XY: 74266

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.592

Alfa AF: 0.683 Hom.: 16636

Bravo AF: 0.571

Asia WGS AF: 0.560 AC: 1950 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs955427; hg19: chr18-58890073;