1-236785242-A-G

Variant names:

• chr1-236785242-A-G
• rs7556238

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 0.844 in 152,148 control chromosomes in the GnomAD database, including 54,600 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 0.84 (54600 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 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: 0.844 AC: 128339 AN: 152030 Hom.: 54556 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.844 AC: 128442 AN: 152148 Hom.: 54600 Cov.: 32 AF XY: 0.843 AC XY: 62678 AN XY: 74386

African (AFR) AF: 0.751 AC: 31135 AN: 41478

American (AMR) AF: 0.864 AC: 13210 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3133 AN: 3470

East Asian (EAS) AF: 0.734 AC: 3787 AN: 5156

South Asian (SAS) AF: 0.837 AC: 4039 AN: 4824

European-Finnish (FIN) AF: 0.862 AC: 9129 AN: 10592

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61142 AN: 68014

Other (OTH) AF: 0.840 AC: 1775 AN: 2114

Alfa AF: 0.884 Hom.: 36325

Bravo AF: 0.841

Asia WGS AF: 0.769 AC: 2675 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	0.80
DANN	Benign	0.62
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs7556238; hg19: chr1-236948542;