rs7552167

Variant names:

• chr1-24192153-A-G
• rs7552167

Your query was ambiguous. Multiple possible variants found:

• chr1-24192153-A-G
• chr1-24192153-A-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 0.867 in 152,248 control chromosomes in the GnomAD database, including 57,281 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 0.87 (57281 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.894 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: 0.867 AC: 131851 AN: 152130 Hom.: 57229 Cov.: 33

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.867 AC: 131957 AN: 152248 Hom.: 57281 Cov.: 33 AF XY: 0.866 AC XY: 64497 AN XY: 74434

African (AFR) AF: 0.889 AC: 36937 AN: 41534

American (AMR) AF: 0.906 AC: 13861 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2935 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3928 AN: 5178

South Asian (SAS) AF: 0.884 AC: 4274 AN: 4834

European-Finnish (FIN) AF: 0.825 AC: 8738 AN: 10592

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58453 AN: 68022

Other (OTH) AF: 0.845 AC: 1789 AN: 2116

Alfa AF: 0.866 Hom.: 190275

Bravo AF: 0.873

Asia WGS AF: 0.780 AC: 2712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.69
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs7552167; hg19: chr1-24518643; COSMIC: COSV59525825;