rs9396503

Variant names:

• chr6-14535858-C-A
• rs9396503
• ENST00000729738.1:n.373+61656G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-14535858-C-A
• chr6-14535858-C-G

Variant summary

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

The ENST00000729738.1(ENSG00000234261):​n.373+61656G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,970 control chromosomes in the GnomAD database, including 19,555 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 (19555 hom., cov: 32)
• Consequence: ENSG00000234261 ENST00000729738.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 1 publications found

Genes affected

ENSG00000234261 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729738.1. 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
	ENSG00000234261	ENST00000729738.1		n.373+61656G>T		intron	N/A
	ENSG00000234261	ENST00000729739.1		n.309+61656G>T		intron	N/A
	ENSG00000234261	ENST00000729740.1		n.270+61656G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72623 AN: 151852 Hom.: 19502 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.479 AC: 72747 AN: 151970 Hom.: 19555 Cov.: 32 AF XY: 0.480 AC XY: 35652 AN XY: 74278

African (AFR) AF: 0.717 AC: 29725 AN: 41440

American (AMR) AF: 0.452 AC: 6905 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3466

East Asian (EAS) AF: 0.653 AC: 3357 AN: 5142

South Asian (SAS) AF: 0.558 AC: 2692 AN: 4824

European-Finnish (FIN) AF: 0.354 AC: 3741 AN: 10568

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23911 AN: 67948

Other (OTH) AF: 0.414 AC: 873 AN: 2110

Alfa AF: 0.400 Hom.: 37184

Bravo AF: 0.497

Asia WGS AF: 0.614 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.57
DANN	Benign	0.23
PhyloP100		0.26

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: rs9396503;

hg19: chr6-14536089;