rs3104401

Variant names:

• chr6-32719581-A-G
• rs3104401

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 0.138 in 151,792 control chromosomes in the GnomAD database, including 1,670 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 0.14 (1670 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 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: 0.138 AC: 20928 AN: 151674 Hom.: 1669 Cov.: 29

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0606

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.138 AC: 20944 AN: 151792 Hom.: 1670 Cov.: 29 AF XY: 0.138 AC XY: 10229 AN XY: 74152

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.179

Alfa AF: 0.140 Hom.: 2109

Bravo AF: 0.144

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	10
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3104401; hg19: chr6-32687358;