chr6-160701755-G-A

Variant names:

• chr6-160701755-G-A
• rs2314852
• ENST00000448126.6:n.1551G>A

Variant summary

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

The ENST00000448126.6(ENSG00000224477):​n.1551G>A 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 0.78 in 152,124 control chromosomes in the GnomAD database, including 47,333 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 0.78 (47333 hom., cov: 31)
• Consequence: ENSG00000224477 ENST00000448126.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.33
• Publications: 9 publications found

Genes affected

ENSG00000224477 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448126.6. 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
	ENSG00000224477	ENST00000448126.6	TSL:5	n.1551G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118523 AN: 152006 Hom.: 47285 Cov.: 31

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.780 AC: 118625 AN: 152124 Hom.: 47333 Cov.: 31 AF XY: 0.770 AC XY: 57233 AN XY: 74348

African (AFR) AF: 0.868 AC: 36016 AN: 41512

American (AMR) AF: 0.625 AC: 9553 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2709 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1862 AN: 5156

South Asian (SAS) AF: 0.575 AC: 2774 AN: 4826

European-Finnish (FIN) AF: 0.805 AC: 8501 AN: 10564

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54692 AN: 67994

Other (OTH) AF: 0.763 AC: 1612 AN: 2112

Alfa AF: 0.755 Hom.: 2371

Bravo AF: 0.769

Asia WGS AF: 0.531 AC: 1850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0030
DANN	Benign	0.46
PhyloP100		-5.3
PromoterAI		0.020	Neutral

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: rs2314852;

hg19: chr6-161122787;

COSMIC: COSV51985910;