rs1388930

Variant names:

• chr6-50438862-A-G
• rs1388930
• ENST00000758915.1:n.84+17480A>G

Variant summary

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

The ENST00000758915.1(ENSG00000233470):​n.84+17480A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,128 control chromosomes in the GnomAD database, including 5,155 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 0.23 (5155 hom., cov: 32)
• Consequence: ENSG00000233470 ENST00000758915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534
• Publications: 1 publications found

Genes affected

ENSG00000233470 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758915.1. 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
	ENSG00000233470	ENST00000758915.1		n.84+17480A>G		intron	N/A
	ENSG00000233470	ENST00000758916.1		n.84+17480A>G		intron	N/A
	ENSG00000233470	ENST00000758917.1		n.85-9595A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35181 AN: 152010 Hom.: 5150 Cov.: 32

Gnomad AFR AF: 0.0858

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.231 AC: 35208 AN: 152128 Hom.: 5155 Cov.: 32 AF XY: 0.244 AC XY: 18123 AN XY: 74372

African (AFR) AF: 0.0859 AC: 3569 AN: 41534

American (AMR) AF: 0.374 AC: 5712 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 999 AN: 3468

East Asian (EAS) AF: 0.561 AC: 2886 AN: 5142

South Asian (SAS) AF: 0.413 AC: 1992 AN: 4818

European-Finnish (FIN) AF: 0.304 AC: 3225 AN: 10594

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15953 AN: 67976

Other (OTH) AF: 0.234 AC: 494 AN: 2112

Alfa AF: 0.245 Hom.: 9748

Bravo AF: 0.232

Asia WGS AF: 0.475 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.75
PhyloP100		-0.53

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: rs1388930;

hg19: chr6-50406575;