rs10493643

chr1-79887054-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 0.0722 in 151,890 control chromosomes in the GnomAD database, including 497 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 0.072 (497 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 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: 0.0722 AC: 10958 AN: 151772 Hom.: 495 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.0462

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.0367

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0722 AC: 10966 AN: 151890 Hom.: 497 Cov.: 33 AF XY: 0.0722 AC XY: 5359 AN XY: 74196

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0461

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.0366

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0288

Gnomad4 NFE AF: 0.0550

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.0656 Hom.: 183

Bravo AF: 0.0729

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.10
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493643; hg19: chr1-80352739;