chr6-126643364-A-G

Position:

• chr6-126643364-A-G

Variant summary

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

The ENST00000651326.1(ENSG00000293110):​n.694-39899T>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 0.281 in 399,210 control chromosomes in the GnomAD database, including 17,934 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 0.24 (5356 hom., cov: 32)
  • Exomes 𝑓: 0.30 (12578 hom.)
• Consequence: ENST00000651326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651326.1	n.694-39899T>C		intron_variant, non_coding_transcript_variant
	ENST00000650727.1	n.1167-21491T>C		intron_variant, non_coding_transcript_variant
	ENST00000652545.1	n.1477-21491T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36841 AN: 152054 Hom.: 5354 Cov.: 32

Gnomad AFR AF: 0.0878

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.285

GnomAD4 exome AF: 0.305 AC: 75316 AN: 247038 Hom.: 12578 AF XY: 0.309 AC XY: 40156 AN XY: 130068

Gnomad4 AFR exome AF: 0.105

Gnomad4 AMR exome AF: 0.471

Gnomad4 ASJ exome AF: 0.325

Gnomad4 EAS exome AF: 0.467

Gnomad4 SAS exome AF: 0.381

Gnomad4 FIN exome AF: 0.272

Gnomad4 NFE exome AF: 0.274

Gnomad4 OTH exome AF: 0.301

GnomAD4 genome AF: 0.242 AC: 36850 AN: 152172 Hom.: 5356 Cov.: 32 AF XY: 0.249 AC XY: 18545 AN XY: 74430

Gnomad4 AFR AF: 0.0878

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.282

Alfa AF: 0.278 Hom.: 13798

Bravo AF: 0.250

Asia WGS AF: 0.354 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4273712; hg19: chr6-126964510; COSMIC: COSV69095953;