rs7452888

Variant names:

• chr6-169296169-A-G
• rs7452888

Your query was ambiguous. Multiple possible variants found:

• chr6-169296169-A-G
• chr6-169296169-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 0.575 in 152,108 control chromosomes in the GnomAD database, including 25,665 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 0.57 (25665 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 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: 0.575 AC: 87363 AN: 151990 Hom.: 25638 Cov.: 33

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.575 AC: 87446 AN: 152108 Hom.: 25665 Cov.: 33 AF XY: 0.577 AC XY: 42931 AN XY: 74364

African (AFR) AF: 0.663 AC: 27505 AN: 41496

American (AMR) AF: 0.576 AC: 8802 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1607 AN: 3468

East Asian (EAS) AF: 0.793 AC: 4110 AN: 5184

South Asian (SAS) AF: 0.613 AC: 2955 AN: 4820

European-Finnish (FIN) AF: 0.539 AC: 5699 AN: 10570

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34936 AN: 67972

Other (OTH) AF: 0.547 AC: 1156 AN: 2112

Alfa AF: 0.541 Hom.: 16661

Bravo AF: 0.583

Asia WGS AF: 0.720 AC: 2502 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	3.3
DANN	Benign	0.70
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7452888; hg19: chr6-169696264;