rs9384488

Variant names:

• chr6-156688247-G-A
• rs9384488
• ENST00000743650.1:n.77-7702C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-156688247-G-A
• chr6-156688247-G-C
• chr6-156688247-G-T

Variant summary

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

The ENST00000743650.1(ENSG00000296922):​n.77-7702C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,102 control chromosomes in the GnomAD database, including 20,525 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 0.48 (20525 hom., cov: 32)
• Consequence: ENSG00000296922 ENST00000743650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72
• Publications: 8 publications found

Genes affected

ENSG00000296922 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743650.1. 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
	ENSG00000296922	ENST00000743650.1		n.77-7702C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72827 AN: 151982 Hom.: 20476 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.480 AC: 72933 AN: 152102 Hom.: 20525 Cov.: 32 AF XY: 0.477 AC XY: 35439 AN XY: 74368

African (AFR) AF: 0.786 AC: 32623 AN: 41500

American (AMR) AF: 0.340 AC: 5204 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1403 AN: 3472

East Asian (EAS) AF: 0.562 AC: 2909 AN: 5172

South Asian (SAS) AF: 0.497 AC: 2395 AN: 4822

European-Finnish (FIN) AF: 0.299 AC: 3158 AN: 10570

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23827 AN: 67966

Other (OTH) AF: 0.435 AC: 917 AN: 2108

Alfa AF: 0.385 Hom.: 21154

Bravo AF: 0.493

Asia WGS AF: 0.599 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.029
DANN	Benign	0.32
PhyloP100		-2.7

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: rs9384488;

hg19: chr6-157009381;