rs2410618

Variant names:

• chr8-19995989-G-A
• rs2410618

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 0.257 in 152,028 control chromosomes in the GnomAD database, including 5,067 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 0.26 (5067 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39029 AN: 151910 Hom.: 5067 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.257 AC: 39040 AN: 152028 Hom.: 5067 Cov.: 33 AF XY: 0.256 AC XY: 19037 AN XY: 74272

African (AFR) AF: 0.240 AC: 9930 AN: 41438

American (AMR) AF: 0.242 AC: 3703 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1177 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1070 AN: 5176

South Asian (SAS) AF: 0.250 AC: 1205 AN: 4816

European-Finnish (FIN) AF: 0.248 AC: 2616 AN: 10544

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18367 AN: 67994

Other (OTH) AF: 0.253 AC: 531 AN: 2102

Alfa AF: 0.253 Hom.: 1117

Bravo AF: 0.254

Asia WGS AF: 0.254 AC: 883 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.47
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2410618; hg19: chr8-19853500;