rs7547072

Positions:

• chr1-154666779-C-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 0.453 in 151,750 control chromosomes in the GnomAD database, including 16,215 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 0.45 (16215 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68725 AN: 151628 Hom.: 16207 Cov.: 30

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.453 AC: 68761 AN: 151750 Hom.: 16215 Cov.: 30 AF XY: 0.454 AC XY: 33692 AN XY: 74130

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.447

Alfa AF: 0.491 Hom.: 20381

Bravo AF: 0.451

Asia WGS AF: 0.486 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7547072; hg19: chr1-154639255;