6-18349135-C-T

Variant names:

• chr6-18349135-C-T
• rs1408445
• ENST00000790360.1:n.722-33761C>T

Variant summary

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

The ENST00000790360.1(ENSG00000289097):​n.722-33761C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,296 control chromosomes in the GnomAD database, including 60,051 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 0.89 (60051 hom., cov: 34)
• Consequence: ENSG00000289097 ENST00000790360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 1 publications found

Genes affected

ENSG00000289097 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790360.1. 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
	ENSG00000289097	ENST00000790360.1		n.722-33761C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.887 AC: 135029 AN: 152178 Hom.: 60003 Cov.: 34

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.887 AC: 135133 AN: 152296 Hom.: 60051 Cov.: 34 AF XY: 0.891 AC XY: 66371 AN XY: 74478

African (AFR) AF: 0.859 AC: 35689 AN: 41540

American (AMR) AF: 0.900 AC: 13772 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3073 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5179 AN: 5190

South Asian (SAS) AF: 0.940 AC: 4540 AN: 4832

European-Finnish (FIN) AF: 0.928 AC: 9850 AN: 10618

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 60021 AN: 68022

Other (OTH) AF: 0.882 AC: 1862 AN: 2112

Alfa AF: 0.884 Hom.: 91736

Bravo AF: 0.885

Asia WGS AF: 0.964 AC: 3351 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.26
PhyloP100		-0.12

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: rs1408445;

hg19: chr6-18349366;