6-139956842-C-T

Variant names:

• chr6-139956842-C-T
• rs11754461
• ENST00000666152.2:n.748-17384G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000666152.2(ENSG00000287820):​n.748-17384G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00431 in 150,806 control chromosomes in the GnomAD database, including 1 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 0.0043 (1 hom., cov: 31)
• Consequence: ENSG00000287820 ENST00000666152.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 1 publications found

Genes affected

ENSG00000287820 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666152.2. 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
	ENSG00000287820	ENST00000666152.2		n.748-17384G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00431 AC: 650 AN: 150690 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.00406

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00179

Gnomad ASJ AF: 0.00549

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000210

Gnomad FIN AF: 0.000786

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00628

Gnomad OTH AF: 0.00145

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

GnomAD4 genome AF: 0.00431 AC: 650 AN: 150806 Hom.: 1 Cov.: 31 AF XY: 0.00378 AC XY: 278 AN XY: 73590

African (AFR) AF: 0.00404 AC: 166 AN: 41050

American (AMR) AF: 0.00178 AC: 27 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.00549 AC: 19 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5128

South Asian (SAS) AF: 0.000210 AC: 1 AN: 4760

European-Finnish (FIN) AF: 0.000786 AC: 8 AN: 10178

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.00628 AC: 426 AN: 67806

Other (OTH) AF: 0.00144 AC: 3 AN: 2088

Alfa AF: 0.00431 Hom.: 0

Bravo AF: 0.00463

Asia WGS AF: 0.000289 AC: 1 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	1.6
DANN	Benign	0.23
PhyloP100		-0.36

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: rs11754461;

hg19: chr6-140277979;