rs4286900

Variant names:

• chr7-52237510-G-A
• rs4286900

Your query was ambiguous. Multiple possible variants found:

• chr7-52237510-G-A
• chr7-52237510-G-T

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 0.368 in 151,816 control chromosomes in the GnomAD database, including 12,331 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 0.37 (12331 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 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: 0.368 AC: 55832 AN: 151698 Hom.: 12327 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.368 AC: 55853 AN: 151816 Hom.: 12331 Cov.: 32 AF XY: 0.384 AC XY: 28493 AN XY: 74200

African (AFR) AF: 0.123 AC: 5115 AN: 41456

American (AMR) AF: 0.434 AC: 6621 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1485 AN: 3466

East Asian (EAS) AF: 0.437 AC: 2261 AN: 5174

South Asian (SAS) AF: 0.530 AC: 2550 AN: 4810

European-Finnish (FIN) AF: 0.676 AC: 7064 AN: 10452

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29485 AN: 67900

Other (OTH) AF: 0.348 AC: 733 AN: 2108

Alfa AF: 0.399 Hom.: 34119

Bravo AF: 0.336

Asia WGS AF: 0.442 AC: 1528 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.35
DANN	Benign	0.58
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs4286900; hg19: chr7-52305206;