1-234697114-G-A

Variant names:

• chr1-234697114-G-A
• rs10495350

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 0.068 in 152,254 control chromosomes in the GnomAD database, including 475 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 0.068 (475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0679 AC: 10329 AN: 152136 Hom.: 471 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.0741

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.0613

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.0561

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0453

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0680 AC: 10355 AN: 152254 Hom.: 475 Cov.: 32 AF XY: 0.0675 AC XY: 5026 AN XY: 74450

African (AFR) AF: 0.116 AC: 4815 AN: 41542

American (AMR) AF: 0.0742 AC: 1135 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0236 AC: 82 AN: 3468

East Asian (EAS) AF: 0.0610 AC: 316 AN: 5178

South Asian (SAS) AF: 0.0323 AC: 156 AN: 4830

European-Finnish (FIN) AF: 0.0561 AC: 594 AN: 10596

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0454 AC: 3085 AN: 68020

Other (OTH) AF: 0.0539 AC: 114 AN: 2114

Alfa AF: 0.0536 Hom.: 381

Bravo AF: 0.0731

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.058
DANN	Benign	0.17
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10495350; hg19: chr1-234832861;