rs41489451

Variant names:

• chr6-32602171-G-T
• rs41489451

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 0.0433 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
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0475 AC: 1960 AN: 41244

American (AMR) AF: 0.0710 AC: 1082 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.00779 AC: 27 AN: 3466

East Asian (EAS) AF: 0.0163 AC: 83 AN: 5082

South Asian (SAS) AF: 0.0113 AC: 54 AN: 4794

European-Finnish (FIN) AF: 0.112 AC: 1180 AN: 10548

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0308 AC: 2095 AN: 67952

Other (OTH) AF: 0.0323 AC: 68 AN: 2106

Alfa AF: 0.0365 Hom.: 44

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
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs41489451; hg19: chr6-32569948;