rs4286900

Positions:

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

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 0.368 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.348

Alfa AF: 0.415 Hom.: 21052

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4286900; hg19: chr7-52305206;