1-92795004-T-C

Variant names:

• chr1-92795004-T-C
• rs7543964

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;