1-90361374-T-C

Variant names:

• chr1-90361374-T-C
• rs1396315

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 0.291 in 152,100 control chromosomes in the GnomAD database, including 7,318 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 0.29 (7318 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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: 0.291 AC: 44237 AN: 151982 Hom.: 7292 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.291 AC: 44309 AN: 152100 Hom.: 7318 Cov.: 32 AF XY: 0.295 AC XY: 21910 AN XY: 74354

African (AFR) AF: 0.437 AC: 18106 AN: 41476

American (AMR) AF: 0.241 AC: 3674 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 975 AN: 3468

East Asian (EAS) AF: 0.510 AC: 2637 AN: 5170

South Asian (SAS) AF: 0.257 AC: 1241 AN: 4824

European-Finnish (FIN) AF: 0.269 AC: 2843 AN: 10584

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14215 AN: 67990

Other (OTH) AF: 0.245 AC: 518 AN: 2110

Alfa AF: 0.227 Hom.: 7146

Bravo AF: 0.294

Asia WGS AF: 0.343 AC: 1190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.4
DANN	Benign	0.73
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1396315; hg19: chr1-90826932;