1-92795004-T-C

Variant names:

• chr1-92795004-T-C
• rs7543964

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.888 AC: 36840 AN: 41504

American (AMR) AF: 0.929 AC: 14198 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3335 AN: 3470

East Asian (EAS) AF: 0.971 AC: 5019 AN: 5168

South Asian (SAS) AF: 0.966 AC: 4671 AN: 4834

European-Finnish (FIN) AF: 0.884 AC: 9359 AN: 10586

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61291 AN: 68022

Other (OTH) AF: 0.903 AC: 1908 AN: 2112

Alfa AF: 0.906 Hom.: 10869

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
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs7543964; hg19: chr1-93260561;