rs7547072

Variant names:

• chr1-154666779-C-T
• rs7547072

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 0.453 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.332 AC: 13749 AN: 41384

American (AMR) AF: 0.501 AC: 7655 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1716 AN: 3468

East Asian (EAS) AF: 0.538 AC: 2773 AN: 5152

South Asian (SAS) AF: 0.486 AC: 2282 AN: 4700

European-Finnish (FIN) AF: 0.462 AC: 4861 AN: 10520

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34129 AN: 67940

Other (OTH) AF: 0.447 AC: 944 AN: 2112

Alfa AF: 0.477 Hom.: 27173

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
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs7547072; hg19: chr1-154639255;