rs6774870

chr3-89515741-C-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 0.25 in 152,018 control chromosomes in the GnomAD database, including 5,090 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 0.25 (5090 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 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: 0.250 AC: 37913 AN: 151900 Hom.: 5089 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0859

Gnomad SAS AF: 0.0934

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.250 AC: 37937 AN: 152018 Hom.: 5090 Cov.: 32 AF XY: 0.250 AC XY: 18552 AN XY: 74278

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0863

Gnomad4 SAS AF: 0.0929

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.213

Alfa AF: 0.254 Hom.: 2806

Bravo AF: 0.237

Asia WGS AF: 0.0970 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.33
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: rs6774870; hg19: chr3-89564891;