rs1678618

Variant names:

• chr10-72046530-A-G
• rs1678618

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 0.39 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.248 AC: 10257 AN: 41366

American (AMR) AF: 0.392 AC: 5957 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1770 AN: 3468

East Asian (EAS) AF: 0.112 AC: 579 AN: 5160

South Asian (SAS) AF: 0.296 AC: 1422 AN: 4808

European-Finnish (FIN) AF: 0.431 AC: 4526 AN: 10506

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33148 AN: 67932

Other (OTH) AF: 0.430 AC: 904 AN: 2104

Alfa AF: 0.453 Hom.: 58015

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
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs1678618; hg19: chr10-73806288;