1-228073027-C-T

Variant names:

• chr1-228073027-C-T
• rs1188977

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 0.159 in 152,206 control chromosomes in the GnomAD database, including 2,914 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 0.16 (2914 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165

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 (AFR) allele frequency at 95% confidence interval = 0.324 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: 0.159 AC: 24116 AN: 152088 Hom.: 2907 Cov.: 33

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0758

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.159 AC: 24152 AN: 152206 Hom.: 2914 Cov.: 33 AF XY: 0.158 AC XY: 11766 AN XY: 74418

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0758

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.0981

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0784

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0875 Hom.: 1027

Bravo AF: 0.171

Asia WGS AF: 0.164 AC: 570 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	3.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1188977; hg19: chr1-228260728;