rs41489451

chr6-32602171-G-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 0.0433 in 151,644 control chromosomes in the GnomAD database, including 210 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 0.043 (210 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0674 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: 0.0433 AC: 6565 AN: 151526 Hom.: 209 Cov.: 31

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0705

Gnomad ASJ AF: 0.00779

Gnomad EAS AF: 0.0163

Gnomad SAS AF: 0.0119

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0326

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

GnomAD4 genome AF: 0.0433 AC: 6571 AN: 151644 Hom.: 210 Cov.: 31 AF XY: 0.0463 AC XY: 3429 AN XY: 74098

Gnomad4 AFR AF: 0.0475

Gnomad4 AMR AF: 0.0710

Gnomad4 ASJ AF: 0.00779

Gnomad4 EAS AF: 0.0163

Gnomad4 SAS AF: 0.0113

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0308

Gnomad4 OTH AF: 0.0323

Alfa AF: 0.0365 Hom.: 15

Asia WGS AF: 0.0240 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.8
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41489451; hg19: chr6-32569948;