1-228073027-C-T

Variant names:

• chr1-228073027-C-T
• rs1188977

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 0.159 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.328 AC: 13624 AN: 41494

American (AMR) AF: 0.120 AC: 1839 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0758 AC: 263 AN: 3468

East Asian (EAS) AF: 0.233 AC: 1202 AN: 5168

South Asian (SAS) AF: 0.0981 AC: 473 AN: 4824

European-Finnish (FIN) AF: 0.102 AC: 1085 AN: 10612

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0784 AC: 5332 AN: 68018

Other (OTH) AF: 0.132 AC: 278 AN: 2112

Alfa AF: 0.0946 Hom.: 1782

Bravo AF: 0.171

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
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: rs1188977; hg19: chr1-228260728;