rs2410618

chr8-19995989-G-A

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 0.257 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.253

Alfa AF: 0.259 Hom.: 644

Bravo AF: 0.254

Asia WGS AF: 0.254 AC: 883 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.58
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2410618; hg19: chr8-19853500;