rs1406891

Variant names:

• chr6-160766048-T-C
• rs1406891
• ENST00000785031.1:n.1190A>G

Variant summary

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

The ENST00000785031.1(ENSG00000287558):​n.1190A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 152,064 control chromosomes in the GnomAD database, including 28,801 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 0.61 (28801 hom., cov: 33)
• Consequence: ENSG00000287558 ENST00000785031.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 10 publications found

Genes affected

ENSG00000287558 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785031.1. 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
	ENSG00000287558	ENST00000785031.1		n.1190A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000287558	ENST00000659713.1		n.77+1366A>G		intron	N/A
	ENSG00000287558	ENST00000785027.1		n.190+985A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92441 AN: 151946 Hom.: 28752 Cov.: 33

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.609 AC: 92546 AN: 152064 Hom.: 28801 Cov.: 33 AF XY: 0.615 AC XY: 45708 AN XY: 74336

African (AFR) AF: 0.649 AC: 26897 AN: 41474

American (AMR) AF: 0.701 AC: 10718 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1995 AN: 3470

East Asian (EAS) AF: 0.983 AC: 5095 AN: 5184

South Asian (SAS) AF: 0.715 AC: 3445 AN: 4818

European-Finnish (FIN) AF: 0.535 AC: 5656 AN: 10576

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.540 AC: 36688 AN: 67952

Other (OTH) AF: 0.638 AC: 1344 AN: 2106

Alfa AF: 0.577 Hom.: 12798

Bravo AF: 0.623

Asia WGS AF: 0.838 AC: 2908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		-0.28

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: rs1406891;

hg19: chr6-161187080;