6-26288975-T-C

Position:

• chr6-26288975-T-C

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+164804T>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 0.538 in 151,990 control chromosomes in the GnomAD database, including 23,036 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 0.54 (23036 hom., cov: 32)
• Consequence: ENST00000707189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.89

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901287	XR_007059520.1	n.374+2922T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000707189.1	n.999+164804T>C		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1000+130854T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81792 AN: 151874 Hom.: 23030 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.538 AC: 81838 AN: 151990 Hom.: 23036 Cov.: 32 AF XY: 0.552 AC XY: 41021 AN XY: 74272

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.571

Alfa AF: 0.550 Hom.: 11502

Bravo AF: 0.525

Asia WGS AF: 0.734 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6939589; hg19: chr6-26289203; COSMIC: COSV56805729;