7-27165663-A-G

Position:

• chr7-27165663-A-G

Variant summary

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

The ENST00000470747.4(ENSG00000257184):​c.11-696T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 687,948 control chromosomes in the GnomAD database, including 188,751 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 0.73 (40339 hom., cov: 35)
  • Exomes 𝑓: 0.74 (148412 hom.)
• Consequence: ENSG00000257184 ENST00000470747.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20

Genes affected

ENSG00000257184 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HOXA10-HOXA9	NR_037940.1	n.617-696T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000257184	ENST00000470747.4	c.11-696T>C		intron_variant		3		ENSP00000421799.3

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110591 AN: 152126 Hom.: 40318 Cov.: 35

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.735

GnomAD4 exome AF: 0.743 AC: 397806 AN: 535704 Hom.: 148412 AF XY: 0.747 AC XY: 205025 AN XY: 274554

Gnomad4 AFR exome AF: 0.725

Gnomad4 AMR exome AF: 0.664

Gnomad4 ASJ exome AF: 0.773

Gnomad4 EAS exome AF: 0.677

Gnomad4 SAS exome AF: 0.810

Gnomad4 FIN exome AF: 0.696

Gnomad4 NFE exome AF: 0.746

Gnomad4 OTH exome AF: 0.734

GnomAD4 genome AF: 0.727 AC: 110660 AN: 152244 Hom.: 40339 Cov.: 35 AF XY: 0.726 AC XY: 54018 AN XY: 74434

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.735

Alfa AF: 0.741 Hom.: 40066

Bravo AF: 0.722

Asia WGS AF: 0.723 AC: 2517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	19
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3801776; hg19: chr7-27205282;