17-7242662-T-C

Position:

• chr17-7242662-T-C

Variant summary

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

The ENST00000570760.2(ENSG00000262526):​n.84-983A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 376,770 control chromosomes in the GnomAD database, including 21,885 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 0.30 (7586 hom., cov: 33)
  • Exomes 𝑓: 0.35 (14299 hom.)
• Consequence: ENSG00000262526 ENST00000570760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

Genes affected

ENSG00000262526 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.7242662T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000262526	ENST00000570760.2	n.84-983A>G		intron_variant		3		ENSP00000466023.1
ENSG00000279641	ENST00000624722.1	n.463T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45763 AN: 152054 Hom.: 7594 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.301

GnomAD4 exome AF: 0.350 AC: 78528 AN: 224598 Hom.: 14299 Cov.: 0 AF XY: 0.348 AC XY: 41276 AN XY: 118656

Gnomad4 AFR exome AF: 0.146

Gnomad4 AMR exome AF: 0.393

Gnomad4 ASJ exome AF: 0.349

Gnomad4 EAS exome AF: 0.350

Gnomad4 SAS exome AF: 0.338

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.362

Gnomad4 OTH exome AF: 0.344

GnomAD4 genome AF: 0.301 AC: 45745 AN: 152172 Hom.: 7586 Cov.: 33 AF XY: 0.299 AC XY: 22251 AN XY: 74390

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.297

Alfa AF: 0.348 Hom.: 11756

Bravo AF: 0.298

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs222843; hg19: chr17-7145981;