rs1407516

chr6-168727711-G-Cchr6-168727711-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000693564.1(ENSG00000289090):n.187+1237G>C variant causes a intron, non coding transcript 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: ENST00000693564.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.942

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107986550	XR_001743905.2	n.210+1237G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000693564.1	n.187+1237G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.292

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

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1407516; hg19: chr6-169127808;