rs1294404

chr6-6734789-G-Achr6-6734789-G-C

Variant summary

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

The ENST00000689004.1(ENSG00000226281):n.563+10148C>T 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 0.641 in 151,900 control chromosomes in the GnomAD database, including 32,617 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 0.64 (32617 hom., cov: 30)
• Consequence: ENST00000689004.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928004	XR_007059429.1	n.486-22931C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689004.1	n.563+10148C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97328 AN: 151782 Hom.: 32596 Cov.: 30

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.641 AC: 97382 AN: 151900 Hom.: 32617 Cov.: 30 AF XY: 0.630 AC XY: 46774 AN XY: 74222

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.601

Alfa AF: 0.626 Hom.: 5961

Bravo AF: 0.641

Asia WGS AF: 0.327 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.78
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1294404; hg19: chr6-6735022;