1-84075603-T-C

Position:

• chr1-84075603-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 0.374 in 151,992 control chromosomes in the GnomAD database, including 11,926 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 (11926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 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: 0.374 AC: 56767 AN: 151874 Hom.: 11922 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.374 AC: 56778 AN: 151992 Hom.: 11926 Cov.: 32 AF XY: 0.370 AC XY: 27530 AN XY: 74314

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.384

Alfa AF: 0.428 Hom.: 2778

Bravo AF: 0.359

Asia WGS AF: 0.284 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs953197; hg19: chr1-84541286; COSMIC: COSV65771781;