rs4236502

Variant names:

• chr7-86364787-A-C
• rs4236502

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 0.351 in 152,028 control chromosomes in the GnomAD database, including 11,084 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 0.35 (11084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.464 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: 0.351 AC: 53307 AN: 151910 Hom.: 11083 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.351 AC: 53313 AN: 152028 Hom.: 11084 Cov.: 32 AF XY: 0.349 AC XY: 25946 AN XY: 74298

African (AFR) AF: 0.123 AC: 5095 AN: 41544

American (AMR) AF: 0.401 AC: 6112 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1762 AN: 3462

East Asian (EAS) AF: 0.222 AC: 1151 AN: 5174

South Asian (SAS) AF: 0.388 AC: 1873 AN: 4826

European-Finnish (FIN) AF: 0.391 AC: 4130 AN: 10554

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31811 AN: 67892

Other (OTH) AF: 0.391 AC: 826 AN: 2112

Alfa AF: 0.427 Hom.: 45816

Bravo AF: 0.339

Asia WGS AF: 0.293 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs4236502; hg19: chr7-85994103;