chr1-100718269-T-C

Variant names:

• chr1-100718269-T-C
• rs1041163

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 0.177 in 152,134 control chromosomes in the GnomAD database, including 2,603 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 0.18 (2603 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 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: 0.177 AC: 26895 AN: 152016 Hom.: 2598 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.177 AC: 26914 AN: 152134 Hom.: 2603 Cov.: 32 AF XY: 0.176 AC XY: 13104 AN XY: 74364

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.222

Alfa AF: 0.169 Hom.: 4743

Bravo AF: 0.191

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1041163; hg19: chr1-101183825;