rs2628235

Variant names:

• chr18-65915435-G-C
• rs2628235

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 0.888 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
• Publications: 0 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.724 AC: 29988 AN: 41420

American (AMR) AF: 0.930 AC: 14087 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3215 AN: 3458

East Asian (EAS) AF: 0.989 AC: 5099 AN: 5158

South Asian (SAS) AF: 0.861 AC: 4157 AN: 4828

European-Finnish (FIN) AF: 0.966 AC: 10253 AN: 10616

Middle Eastern (MID) AF: 0.901 AC: 263 AN: 292

European-Non Finnish (NFE) AF: 0.959 AC: 64849 AN: 67638

Other (OTH) AF: 0.905 AC: 1903 AN: 2102

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
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs2628235; hg19: chr18-63582671;