chr1-111244450-C-T

Variant names:

• chr1-111244450-C-T
• rs10494129

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 0.113 in 152,192 control chromosomes in the GnomAD database, including 1,324 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 0.11 (1324 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.197 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: 0.113 AC: 17236 AN: 152074 Hom.: 1321 Cov.: 33

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0923

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.0949

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

GnomAD4 genome AF: 0.113 AC: 17247 AN: 152192 Hom.: 1324 Cov.: 33 AF XY: 0.113 AC XY: 8427 AN XY: 74398

African (AFR) AF: 0.0286 AC: 1189 AN: 41526

American (AMR) AF: 0.203 AC: 3107 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3470

East Asian (EAS) AF: 0.0925 AC: 479 AN: 5180

South Asian (SAS) AF: 0.155 AC: 747 AN: 4822

European-Finnish (FIN) AF: 0.0790 AC: 838 AN: 10602

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10150 AN: 67992

Other (OTH) AF: 0.0944 AC: 199 AN: 2108

Alfa AF: 0.132 Hom.: 869

Bravo AF: 0.118

Asia WGS AF: 0.102 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10494129; hg19: chr1-111787072;