rs3904720

Positions:

• chr6-163410655-G-A

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 0.238 in 152,014 control chromosomes in the GnomAD database, including 5,106 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 0.24 (5106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.352 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: 0.238 AC: 36214 AN: 151896 Hom.: 5101 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.238 AC: 36250 AN: 152014 Hom.: 5106 Cov.: 32 AF XY: 0.239 AC XY: 17747 AN XY: 74294

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.237

Alfa AF: 0.229 Hom.: 773

Bravo AF: 0.260

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	14
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3904720; hg19: chr6-163831687;