XR_001745121.2:n.209+24252T>C

Variant names:

• chr7-24295105-A-G
• rs16120
• ENST00000718234.1:n.319+24252T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745121.2(LOC107986777):​n.209+24252T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,042 control chromosomes in the GnomAD database, including 19,885 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 0.51 (19885 hom., cov: 32)
• Consequence: LOC107986777 XR_001745121.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 1 publications found

Genes affected

ENSG00000228944 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718234.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228944	ENST00000718234.1		n.319+24252T>C		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.341+24252T>C		intron	N/A
	ENSG00000228944	ENST00000745513.1		n.309+24252T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76909 AN: 151924 Hom.: 19875 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.506 AC: 76957 AN: 152042 Hom.: 19885 Cov.: 32 AF XY: 0.511 AC XY: 37939 AN XY: 74296

African (AFR) AF: 0.421 AC: 17453 AN: 41472

American (AMR) AF: 0.618 AC: 9458 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1961 AN: 3470

East Asian (EAS) AF: 0.673 AC: 3470 AN: 5154

South Asian (SAS) AF: 0.540 AC: 2603 AN: 4816

European-Finnish (FIN) AF: 0.517 AC: 5456 AN: 10552

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34920 AN: 67972

Other (OTH) AF: 0.509 AC: 1074 AN: 2108

Alfa AF: 0.512 Hom.: 6950

Bravo AF: 0.511

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.49
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs16120; hg19: chr7-24334724;