6-14006007-A-G

Position:

• chr6-14006007-A-G

Variant summary

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

The ENST00000427011.1(ENSG00000233981):​n.62-570A>G 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 0.347 in 151,784 control chromosomes in the GnomAD database, including 9,492 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 0.35 (9492 hom., cov: 31)
• Consequence: ENST00000427011.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 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
	ENST00000427011.1	n.62-570A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52618 AN: 151670 Hom.: 9486 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.347 AC: 52644 AN: 151784 Hom.: 9492 Cov.: 31 AF XY: 0.347 AC XY: 25758 AN XY: 74138

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.379

Alfa AF: 0.373 Hom.: 4950

Bravo AF: 0.338

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	14
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7750009; hg19: chr6-14006238;