1-242601367-T-G

Variant names:

• chr1-242601367-T-G
• rs10926784

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.59 (24553 hom., cov: 18)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.64
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.587 AC: 82029 AN: 139638 Hom.: 24554 Cov.: 18

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.587 AC: 82044 AN: 139724 Hom.: 24553 Cov.: 18 AF XY: 0.587 AC XY: 39414 AN XY: 67132

African (AFR) AF: 0.490 AC: 18147 AN: 37020

American (AMR) AF: 0.514 AC: 7003 AN: 13628

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2496 AN: 3392

East Asian (EAS) AF: 0.694 AC: 3235 AN: 4662

South Asian (SAS) AF: 0.647 AC: 2731 AN: 4218

European-Finnish (FIN) AF: 0.658 AC: 5263 AN: 8000

Middle Eastern (MID) AF: 0.722 AC: 192 AN: 266

European-Non Finnish (NFE) AF: 0.628 AC: 41292 AN: 65778

Other (OTH) AF: 0.579 AC: 1091 AN: 1884

Alfa AF: 0.501 Hom.: 1494

Bravo AF: 0.572

Asia WGS AF: 0.674 AC: 2339 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.037
DANN	Benign	0.34
PhyloP100		-4.6

Splicing

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

Other links and lift over

dbSNP: rs10926784; hg19: chr1-242764669;