1-236311497-T-C

Variant names:

• chr1-236311497-T-C
• rs7554436

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 0.421 in 151,862 control chromosomes in the GnomAD database, including 14,093 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 0.42 (14093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• 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 (NFE) allele frequency at 95% confidence interval = 0.478 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: 0.421 AC: 63920 AN: 151744 Hom.: 14082 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.421 AC: 63969 AN: 151862 Hom.: 14093 Cov.: 32 AF XY: 0.417 AC XY: 30929 AN XY: 74208

African (AFR) AF: 0.391 AC: 16167 AN: 41386

American (AMR) AF: 0.345 AC: 5266 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1518 AN: 3466

East Asian (EAS) AF: 0.0465 AC: 241 AN: 5178

South Asian (SAS) AF: 0.365 AC: 1759 AN: 4822

European-Finnish (FIN) AF: 0.451 AC: 4750 AN: 10522

Middle Eastern (MID) AF: 0.455 AC: 132 AN: 290

European-Non Finnish (NFE) AF: 0.482 AC: 32756 AN: 67904

Other (OTH) AF: 0.426 AC: 900 AN: 2114

Alfa AF: 0.454 Hom.: 25600

Bravo AF: 0.405

Asia WGS AF: 0.206 AC: 721 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	0.13
DANN	Benign	0.45
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7554436; hg19: chr1-236474797;