rs2240571

Positions:

• chr7-12570362-G-C

Variant summary

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

The ENST00000433040.1(ENSG00000225606):​n.674C>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 0.526 in 227,950 control chromosomes in the GnomAD database, including 32,570 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 0.54 (22448 hom., cov: 33)
  • Exomes 𝑓: 0.50 (10122 hom.)
• Consequence: ENSG00000225606 ENST00000433040.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

Genes affected

ENSG00000225606 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986768	XR_007060635.1	n.1866C>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000225606	ENST00000433040.1	n.674C>G		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81785 AN: 151960 Hom.: 22419 Cov.: 33

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.538

GnomAD4 exome AF: 0.501 AC: 38043 AN: 75870 Hom.: 10122 Cov.: 0 AF XY: 0.507 AC XY: 20920 AN XY: 41278

Gnomad4 AFR exome AF: 0.600

Gnomad4 AMR exome AF: 0.425

Gnomad4 ASJ exome AF: 0.487

Gnomad4 EAS exome AF: 0.358

Gnomad4 SAS exome AF: 0.537

Gnomad4 FIN exome AF: 0.475

Gnomad4 NFE exome AF: 0.496

Gnomad4 OTH exome AF: 0.480

GnomAD4 genome AF: 0.538 AC: 81858 AN: 152080 Hom.: 22448 Cov.: 33 AF XY: 0.535 AC XY: 39748 AN XY: 74348

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.532

Alfa AF: 0.533 Hom.: 2679

Bravo AF: 0.537

Asia WGS AF: 0.462 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2240571; hg19: chr7-12609988;