rs1321312

Variant names:

• chr6-36655097-C-G
• rs1321312
• ENST00000778909.1:n.192+5584G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-36655097-C-G
• chr6-36655097-C-T

Variant summary

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

The ENST00000778909.1(ENSG00000301446):​n.192+5584G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.916 in 152,292 control chromosomes in the GnomAD database, including 64,100 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 0.92 (64100 hom., cov: 32)
• Consequence: ENSG00000301446 ENST00000778909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.744
• Publications: 4 publications found

Genes affected

ENSG00000301446 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778909.1. 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
	ENSG00000301446	ENST00000778909.1		n.192+5584G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139375 AN: 152174 Hom.: 64038 Cov.: 32

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.916 AC: 139496 AN: 152292 Hom.: 64100 Cov.: 32 AF XY: 0.913 AC XY: 67968 AN XY: 74448

African (AFR) AF: 0.980 AC: 40736 AN: 41576

American (AMR) AF: 0.905 AC: 13857 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2770 AN: 3472

East Asian (EAS) AF: 0.889 AC: 4603 AN: 5176

South Asian (SAS) AF: 0.935 AC: 4513 AN: 4828

European-Finnish (FIN) AF: 0.870 AC: 9216 AN: 10590

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.894 AC: 60799 AN: 68018

Other (OTH) AF: 0.899 AC: 1900 AN: 2114

Alfa AF: 0.905 Hom.: 7760

Bravo AF: 0.920

Asia WGS AF: 0.931 AC: 3239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.77
PhyloP100		0.74

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: rs1321312;

hg19: chr6-36622874;