rs1678618

Variant names:

• chr10-72046530-A-G
• rs1678618

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 0.39 in 151,760 control chromosomes in the GnomAD database, including 12,506 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 0.39 (12506 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

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 = 0.484 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: 0.390 AC: 59156 AN: 151642 Hom.: 12507 Cov.: 30

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.390 AC: 59154 AN: 151760 Hom.: 12506 Cov.: 30 AF XY: 0.382 AC XY: 28329 AN XY: 74096

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.430

Alfa AF: 0.469 Hom.: 21408

Bravo AF: 0.381

Asia WGS AF: 0.209 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1678618; hg19: chr10-73806288;