rs1407516

Variant names:

• chr6-168727711-G-C
• rs1407516
• ENST00000747060.1:n.294C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-168727711-G-C
• chr6-168727711-G-T

Variant summary

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

The ENST00000747060.1(ENSG00000297313):​n.294C>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 0.293 in 151,970 control chromosomes in the GnomAD database, including 6,960 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 0.29 (6960 hom., cov: 32)
• Consequence: ENSG00000297313 ENST00000747060.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.942
• Publications: 0 publications found

Genes affected

ENSG00000297313 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747060.1. 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
	ENSG00000297313	ENST00000747060.1		n.294C>G		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000289090	ENST00000693564.2		n.246+1237G>C		intron	N/A
	ENSG00000289090	ENST00000746859.1		n.453-421G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44518 AN: 151852 Hom.: 6935 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.293 AC: 44593 AN: 151970 Hom.: 6960 Cov.: 32 AF XY: 0.294 AC XY: 21861 AN XY: 74232

African (AFR) AF: 0.339 AC: 14033 AN: 41428

American (AMR) AF: 0.395 AC: 6038 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 931 AN: 3466

East Asian (EAS) AF: 0.413 AC: 2120 AN: 5128

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4816

European-Finnish (FIN) AF: 0.194 AC: 2056 AN: 10588

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.250 AC: 17005 AN: 67958

Other (OTH) AF: 0.292 AC: 616 AN: 2110

Alfa AF: 0.125 Hom.: 195

Bravo AF: 0.313

Asia WGS AF: 0.422 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.50
PhyloP100		0.94

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: rs1407516;

hg19: chr6-169127808;