rs834789

chr7-136177559-T-C

Variant summary

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

The ENST00000668062.1(ENSG00000232053):n.115-64591T>C 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 0.362 in 152,000 control chromosomes in the GnomAD database, including 12,404 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 0.36 (12403 hom., cov: 32)
  • Exomes 𝑓: 0.36 (1 hom.)
• Consequence: ENST00000668062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375523	XR_007060545.1	n.526+146T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668062.1	n.115-64591T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55027 AN: 151868 Hom.: 12379 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0251

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.326

GnomAD4 exome AF: 0.357 AC: 5 AN: 14 Hom.: 1 AF XY: 0.333 AC XY: 4 AN XY: 12

Gnomad4 NFE exome AF: 0.357

GnomAD4 genome AF: 0.362 AC: 55093 AN: 151986 Hom.: 12403 Cov.: 32 AF XY: 0.356 AC XY: 26485 AN XY: 74312

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.0252

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.323

Alfa AF: 0.314 Hom.: 1383

Bravo AF: 0.372

Asia WGS AF: 0.184 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.12
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs834789; hg19: chr7-135862307;