chr1-242601367-T-G

Position:

• chr1-242601367-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.579

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10926784; hg19: chr1-242764669;