6-126665850-A-G

Position:

• chr6-126665850-A-G

Variant summary

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

The ENST00000651326.1(ENSG00000293110):​n.694-62385T>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 0.813 in 151,980 control chromosomes in the GnomAD database, including 50,598 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 0.81 (50598 hom., cov: 31)
• Consequence: ENST00000651326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377992	XR_001743836.2	n.912+4564A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651326.1	n.694-62385T>C		intron_variant, non_coding_transcript_variant
	ENST00000650727.1	n.1167-43977T>C		intron_variant, non_coding_transcript_variant
	ENST00000652545.1	n.1477-43977T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123445 AN: 151862 Hom.: 50549 Cov.: 31

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.813 AC: 123547 AN: 151980 Hom.: 50598 Cov.: 31 AF XY: 0.817 AC XY: 60691 AN XY: 74258

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.820

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.815

Alfa AF: 0.789 Hom.: 12192

Bravo AF: 0.824

Asia WGS AF: 0.827 AC: 2873 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1262476; hg19: chr6-126986996; COSMIC: COSV60280568;