rs6532197

Variant names:

• chr4-89876150-A-G
• rs6532197

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 0.157 in 152,222 control chromosomes in the GnomAD database, including 3,013 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 0.16 (3013 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 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: 0.157 AC: 23900 AN: 152104 Hom.: 3002 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0902

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.157 AC: 23945 AN: 152222 Hom.: 3013 Cov.: 32 AF XY: 0.154 AC XY: 11453 AN XY: 74416

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.0900

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0569

Gnomad4 NFE AF: 0.0705

Gnomad4 OTH AF: 0.159

Alfa AF: 0.0902 Hom.: 2000

Bravo AF: 0.169

Asia WGS AF: 0.229 AC: 795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6532197; hg19: chr4-90797301;