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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986550	XR_001743905.2	n.210+1237G>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297313	ENST00000747060.1	n.294C>G		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000289090	ENST00000693564.2	n.246+1237G>C		intron_variant	Intron 2 of 3
ENSG00000289090	ENST00000746859.1	n.453-421G>C		intron_variant	Intron 4 of 4
ENSG00000289090	ENST00000746860.1	n.318+1237G>C		intron_variant	Intron 3 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs1407516; hg19: chr6-169127808;