1-96900421-C-T

Variant names:

• chr1-96900421-C-T
• rs2681194

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 0.373 in 151,996 control chromosomes in the GnomAD database, including 11,006 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 0.37 (11006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 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: 0.374 AC: 56738 AN: 151878 Hom.: 11007 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.373 AC: 56742 AN: 151996 Hom.: 11006 Cov.: 32 AF XY: 0.375 AC XY: 27882 AN XY: 74288

African (AFR) AF: 0.257 AC: 10647 AN: 41494

American (AMR) AF: 0.415 AC: 6333 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1233 AN: 3466

East Asian (EAS) AF: 0.435 AC: 2239 AN: 5144

South Asian (SAS) AF: 0.333 AC: 1600 AN: 4810

European-Finnish (FIN) AF: 0.433 AC: 4565 AN: 10542

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.423 AC: 28734 AN: 67962

Other (OTH) AF: 0.372 AC: 785 AN: 2110

Alfa AF: 0.402 Hom.: 21052

Bravo AF: 0.367

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.76
DANN	Benign	0.27
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs2681194; hg19: chr1-97365977; COSMIC: COSV66868348;