rs7556238

Positions:

• chr1-236785242-A-G

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 0.844 in 152,148 control chromosomes in the GnomAD database, including 54,600 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 0.84 (54600 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 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: 0.844 AC: 128339 AN: 152030 Hom.: 54556 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.844 AC: 128442 AN: 152148 Hom.: 54600 Cov.: 32 AF XY: 0.843 AC XY: 62678 AN XY: 74386

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.903

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.840

Alfa AF: 0.882 Hom.: 25338

Bravo AF: 0.841

Asia WGS AF: 0.769 AC: 2675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.80
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7556238; hg19: chr1-236948542;