rs2628235

Positions:

• chr18-65915435-G-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 0.888 in 151,574 control chromosomes in the GnomAD database, including 60,619 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 0.89 (60619 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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: 0.888 AC: 134525 AN: 151456 Hom.: 60588 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.904

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.888 AC: 134610 AN: 151574 Hom.: 60619 Cov.: 32 AF XY: 0.889 AC XY: 65857 AN XY: 74092

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.930

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.959

Gnomad4 OTH AF: 0.905

Alfa AF: 0.922 Hom.: 8100

Bravo AF: 0.879

Asia WGS AF: 0.894 AC: 3099 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.39
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2628235; hg19: chr18-63582671;