rs2675679

Variant names:

• chr10-73898823-G-A
• rs2675679

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 0.424 in 152,040 control chromosomes in the GnomAD database, including 15,274 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 0.42 (15274 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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: 0.424 AC: 64449 AN: 151922 Hom.: 15267 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.424 AC: 64475 AN: 152040 Hom.: 15274 Cov.: 31 AF XY: 0.418 AC XY: 31072 AN XY: 74300

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.491

Alfa AF: 0.500 Hom.: 11426

Bravo AF: 0.415

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2675679; hg19: chr10-75658581;