7-13854651-A-G

Position:

• chr7-13854651-A-G

Variant summary

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

The variant allele was found at a frequency of 0.488 in 151,980 control chromosomes in the GnomAD database, including 18,184 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 0.49 (18183 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.13854651A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000224330	ENST00000434321.1	n.92-29T>C		intron_variant		5
ENSG00000224330	ENST00000654062.1	n.573-29T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74019 AN: 151862 Hom.: 18149 Cov.: 33

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.491

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.488 AC: 74109 AN: 151978 Hom.: 18183 Cov.: 33 AF XY: 0.490 AC XY: 36411 AN XY: 74272

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.494

Alfa AF: 0.452 Hom.: 8100

Bravo AF: 0.483

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1019029; hg19: chr7-13894276;