chr1-190558944-T-C

Variant names:

• chr1-190558944-T-C
• rs12072620

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 0.124 in 152,242 control chromosomes in the GnomAD database, including 1,382 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 0.12 (1382 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.177 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: 0.124 AC: 18840 AN: 152124 Hom.: 1372 Cov.: 32

Gnomad AFR AF: 0.0585

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0972

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0920

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.124 AC: 18861 AN: 152242 Hom.: 1382 Cov.: 32 AF XY: 0.124 AC XY: 9231 AN XY: 74418

African (AFR) AF: 0.0586 AC: 2437 AN: 41562

American (AMR) AF: 0.182 AC: 2788 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0972 AC: 337 AN: 3468

East Asian (EAS) AF: 0.169 AC: 870 AN: 5162

South Asian (SAS) AF: 0.0914 AC: 441 AN: 4824

European-Finnish (FIN) AF: 0.148 AC: 1571 AN: 10600

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.146 AC: 9914 AN: 68020

Other (OTH) AF: 0.121 AC: 255 AN: 2114

Alfa AF: 0.143 Hom.: 323

Bravo AF: 0.129

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs12072620; hg19: chr1-190528074;