rs912056

chr6-6735964-A-T

Variant summary

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

The ENST00000689004.1(ENSG00000226281):n.563+8973T>A 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 0.648 in 152,006 control chromosomes in the GnomAD database, including 33,279 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 0.65 (33279 hom., cov: 31)
• Consequence: ENST00000689004.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928004	XR_007059429.1	n.486-24106T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689004.1	n.563+8973T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98440 AN: 151888 Hom.: 33245 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.648 AC: 98509 AN: 152006 Hom.: 33279 Cov.: 31 AF XY: 0.638 AC XY: 47358 AN XY: 74284

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.604

Alfa AF: 0.646 Hom.: 4027

Bravo AF: 0.646

Asia WGS AF: 0.332 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.037
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs912056; hg19: chr6-6736197;