rs2642265

chr7-24213443-C-Achr7-24213443-C-T

Variant summary

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

The ENST00000439839.1(ENSG00000228944):n.160-16414G>T 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 0.327 in 152,058 control chromosomes in the GnomAD database, including 8,814 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 0.33 (8814 hom., cov: 32)
• Consequence: ENST00000439839.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.210-16414G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000439839.1	n.160-16414G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49619 AN: 151940 Hom.: 8800 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.324

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.327 AC: 49677 AN: 152058 Hom.: 8814 Cov.: 32 AF XY: 0.334 AC XY: 24865 AN XY: 74342

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.326

Alfa AF: 0.299 Hom.: 1259

Bravo AF: 0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.9
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2642265; hg19: chr7-24253062;