1-30627082-C-T

Variant names:

• chr1-30627082-C-T
• rs1188414

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 0.536 in 151,692 control chromosomes in the GnomAD database, including 22,078 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 0.54 (22078 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81314 AN: 151576 Hom.: 22061 Cov.: 30

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.536 AC: 81375 AN: 151692 Hom.: 22078 Cov.: 30 AF XY: 0.536 AC XY: 39734 AN XY: 74104

African (AFR) AF: 0.586 AC: 24192 AN: 41316

American (AMR) AF: 0.530 AC: 8078 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1877 AN: 3468

East Asian (EAS) AF: 0.301 AC: 1551 AN: 5154

South Asian (SAS) AF: 0.585 AC: 2812 AN: 4806

European-Finnish (FIN) AF: 0.514 AC: 5385 AN: 10482

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35770 AN: 67912

Other (OTH) AF: 0.529 AC: 1112 AN: 2104

Alfa AF: 0.525 Hom.: 82443

Bravo AF: 0.539

Asia WGS AF: 0.463 AC: 1609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.4
DANN	Benign	0.35
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1188414; hg19: chr1-31099929;