1-103949659-T-C

Variant names:

• chr1-103949659-T-C
• rs1330388

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 0.421 in 152,098 control chromosomes in the GnomAD database, including 13,806 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 0.42 (13806 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 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: 0.421 AC: 64032 AN: 151980 Hom.: 13791 Cov.: 33

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.421 AC: 64078 AN: 152098 Hom.: 13806 Cov.: 33 AF XY: 0.419 AC XY: 31192 AN XY: 74382

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.435

Alfa AF: 0.436 Hom.: 3330

Bravo AF: 0.438

Asia WGS AF: 0.418 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330388; hg19: chr1-104492281;