rs6774870

Variant names:

• chr3-89515741-C-T
• rs6774870

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 0.25 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.248 AC: 10283 AN: 41454

American (AMR) AF: 0.215 AC: 3272 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3468

East Asian (EAS) AF: 0.0863 AC: 446 AN: 5168

South Asian (SAS) AF: 0.0929 AC: 448 AN: 4824

European-Finnish (FIN) AF: 0.403 AC: 4252 AN: 10558

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18154 AN: 67978

Other (OTH) AF: 0.213 AC: 449 AN: 2110

Alfa AF: 0.255 Hom.: 3837

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6774870; hg19: chr3-89564891;