chr1-100717840-T-C

Variant names:

• chr1-100717840-T-C
• rs1409419

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 0.543 in 151,926 control chromosomes in the GnomAD database, including 22,921 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 0.54 (22921 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981

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 (AMR) allele frequency at 95% confidence interval = 0.628 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: 0.543 AC: 82363 AN: 151808 Hom.: 22893 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.543 AC: 82438 AN: 151926 Hom.: 22921 Cov.: 32 AF XY: 0.546 AC XY: 40541 AN XY: 74242

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.550

Alfa AF: 0.511 Hom.: 19319

Bravo AF: 0.554

Asia WGS AF: 0.516 AC: 1792 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	0.55
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1409419; hg19: chr1-101183396;