1-104717673-A-G

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 0.0374 in 152,038 control chromosomes in the GnomAD database, including 262 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 0.037 (262 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 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: 0.0373 AC: 5669 AN: 151920 Hom.: 262 Cov.: 32

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0735

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0647

Gnomad FIN AF: 0.0203

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00380

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0374 AC: 5681 AN: 152038 Hom.: 262 Cov.: 32 AF XY: 0.0391 AC XY: 2903 AN XY: 74332

Gnomad4 AFR AF: 0.0680

Gnomad4 AMR AF: 0.0736

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.0650

Gnomad4 FIN AF: 0.0203

Gnomad4 NFE AF: 0.00382

Gnomad4 OTH AF: 0.0313

Alfa AF: 0.00526 Hom.: 2

Bravo AF: 0.0452

Asia WGS AF: 0.109 AC: 378 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.53
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494023; hg19: chr1-105260295;