rs4236502

Variant names:

• chr7-86364787-A-C
• rs4236502

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.391

Alfa AF: 0.448 Hom.: 30958

Bravo AF: 0.339

Asia WGS AF: 0.293 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4236502; hg19: chr7-85994103;