rs198284

chr7-24225724-C-T

Variant summary

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

The ENST00000439839.1(ENSG00000228944):n.160-28695G>A 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 0.941 in 152,132 control chromosomes in the GnomAD database, including 67,519 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 0.94 (67519 hom., cov: 30)
• Consequence: ENST00000439839.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.210-28695G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000439839.1	n.160-28695G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143117 AN: 152014 Hom.: 67465 Cov.: 30

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.941 AC: 143231 AN: 152132 Hom.: 67519 Cov.: 30 AF XY: 0.941 AC XY: 69965 AN XY: 74346

Gnomad4 AFR AF: 0.986

Gnomad4 AMR AF: 0.957

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.919

Gnomad4 OTH AF: 0.943

Alfa AF: 0.930 Hom.: 9359

Bravo AF: 0.952

Asia WGS AF: 0.979 AC: 3405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.38
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs198284; hg19: chr7-24265343;