1-92795004-T-C

Position:

• chr1-92795004-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 0.905 in 152,192 control chromosomes in the GnomAD database, including 62,440 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 0.91 (62440 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 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: 0.905 AC: 137675 AN: 152074 Hom.: 62407 Cov.: 31

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.905 AC: 137766 AN: 152192 Hom.: 62440 Cov.: 31 AF XY: 0.907 AC XY: 67480 AN XY: 74404

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.929

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.903

Alfa AF: 0.907 Hom.: 10564

Bravo AF: 0.905

Asia WGS AF: 0.964 AC: 3355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7543964; hg19: chr1-93260561;