7-116210408-T-C

Position:

• chr7-116210408-T-C

Variant summary

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

The ENST00000624389.1(ENSG00000279086):​n.1104A>G 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 0.581 in 245,372 control chromosomes in the GnomAD database, including 42,441 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 0.57 (25061 hom., cov: 35)
  • Exomes 𝑓: 0.60 (17380 hom.)
• Consequence: ENSG00000279086 ENST00000624389.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

Genes affected

ENSG00000279086 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.116210408T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000279086	ENST00000624389.1	n.1104A>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86384 AN: 151968 Hom.: 25010 Cov.: 35

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 0.601 AC: 56047 AN: 93294 Hom.: 17380 Cov.: 0 AF XY: 0.600 AC XY: 28505 AN XY: 47500

Gnomad4 AFR exome AF: 0.497

Gnomad4 AMR exome AF: 0.675

Gnomad4 ASJ exome AF: 0.510

Gnomad4 EAS exome AF: 0.879

Gnomad4 SAS exome AF: 0.568

Gnomad4 FIN exome AF: 0.581

Gnomad4 NFE exome AF: 0.574

Gnomad4 OTH exome AF: 0.590

GnomAD4 genome AF: 0.569 AC: 86487 AN: 152078 Hom.: 25061 Cov.: 35 AF XY: 0.575 AC XY: 42757 AN XY: 74358

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.545

Alfa AF: 0.573 Hom.: 3110

Bravo AF: 0.568

Asia WGS AF: 0.710 AC: 2464 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	17
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1319886; hg19: chr7-115850462; COSMIC: COSV64043800;