rs7452888

chr6-169296169-A-Gchr6-169296169-A-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 0.575 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

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 (EAS) allele frequency at 95% confidence interval = 0.773 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: 0.575 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

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.547

Alfa AF: 0.533 Hom.: 11289

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7452888; hg19: chr6-169696264;