3-177784383-C-A

Variant names:

• chr3-177784383-C-A
• rs6764952
• ENST00000850321.1:n.215+5889G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000850321.1(ENSG00000310482):​n.215+5889G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,020 control chromosomes in the GnomAD database, including 3,958 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 0.22 (3958 hom., cov: 32)
• Consequence: ENSG00000310482 ENST00000850321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 2 publications found

Genes affected

ENSG00000310482 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850321.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310482	ENST00000850321.1		n.215+5889G>T		intron	N/A
	ENSG00000310482	ENST00000850322.1		n.170+3418G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33905 AN: 151902 Hom.: 3946 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.223 AC: 33949 AN: 152020 Hom.: 3958 Cov.: 32 AF XY: 0.226 AC XY: 16784 AN XY: 74294

African (AFR) AF: 0.162 AC: 6703 AN: 41466

American (AMR) AF: 0.310 AC: 4733 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3470

East Asian (EAS) AF: 0.124 AC: 642 AN: 5182

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4816

European-Finnish (FIN) AF: 0.250 AC: 2642 AN: 10554

Middle Eastern (MID) AF: 0.303 AC: 88 AN: 290

European-Non Finnish (NFE) AF: 0.244 AC: 16579 AN: 67950

Other (OTH) AF: 0.220 AC: 464 AN: 2112

Alfa AF: 0.222 Hom.: 2183

Bravo AF: 0.227

Asia WGS AF: 0.190 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.5
DANN	Benign	0.80
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6764952;

hg19: chr3-177502171;