1-30094749-G-A

Variant names:

• chr1-30094749-G-A
• rs910696

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 0.3 in 152,154 control chromosomes in the GnomAD database, including 7,483 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 0.30 (7483 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.965
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.573 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: 0.300 AC: 45606 AN: 152036 Hom.: 7475 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.300 AC: 45634 AN: 152154 Hom.: 7483 Cov.: 33 AF XY: 0.303 AC XY: 22565 AN XY: 74376

African (AFR) AF: 0.229 AC: 9499 AN: 41528

American (AMR) AF: 0.401 AC: 6138 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3472

East Asian (EAS) AF: 0.590 AC: 3042 AN: 5154

South Asian (SAS) AF: 0.363 AC: 1748 AN: 4822

European-Finnish (FIN) AF: 0.297 AC: 3143 AN: 10590

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20553 AN: 67980

Other (OTH) AF: 0.263 AC: 556 AN: 2114

Alfa AF: 0.305 Hom.: 25242

Bravo AF: 0.305

Asia WGS AF: 0.426 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.71
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs910696; hg19: chr1-30567596;