rs10737578

chr1-190014590-T-C

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 0.717 in 151,902 control chromosomes in the GnomAD database, including 40,275 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 0.72 (40275 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 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: 0.717 AC: 108842 AN: 151784 Hom.: 40197 Cov.: 31

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.717 AC: 108986 AN: 151902 Hom.: 40275 Cov.: 31 AF XY: 0.716 AC XY: 53118 AN XY: 74204

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.692

Alfa AF: 0.645 Hom.: 53370

Bravo AF: 0.720

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.77
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10737578; hg19: chr1-189983720;