7-13365039-A-G

Position:

• chr7-13365039-A-G

Variant summary

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

The ENST00000456809.1(ENSG00000237713):​n.11T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 151,922 control chromosomes in the GnomAD database, including 41,945 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 0.74 (41945 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000237713 ENST00000456809.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

ENSG00000237713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986770	XR_001745097.2	n.147+54716A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000237713	ENST00000456809.1	n.11T>C		non_coding_transcript_exon_variant	1/5	5
ENSG00000229618	ENST00000411542.1	n.351+54716A>G		intron_variant		4
ENSG00000229618	ENST00000638964.1	n.723+54716A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111740 AN: 151804 Hom.: 41891 Cov.: 31

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.711

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.736 AC: 111860 AN: 151922 Hom.: 41945 Cov.: 31 AF XY: 0.731 AC XY: 54256 AN XY: 74242

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.713

Alfa AF: 0.671 Hom.: 3474

Bravo AF: 0.744

Asia WGS AF: 0.554 AC: 1923 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2116624; hg19: chr7-13404664;