rs16120

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 ENST00000718234.1(ENSG00000228944):​n.319+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: ENSG00000228944 ENST00000718234.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.209+24252T>C		intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2	n.81-98076T>C		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.209+24252T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228944	ENST00000718234.1	n.319+24252T>C		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745512.1	n.341+24252T>C		intron_variant	Intron 2 of 5
ENSG00000228944	ENST00000745513.1	n.309+24252T>C		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745514.1	n.328+24252T>C		intron_variant	Intron 2 of 2

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 v4.3

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;