rs16119

Variant names:

• chr7-24295311-A-G
• rs16119
• ENST00000718234.1:n.319+24046T>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+24046T>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 152,066 control chromosomes in the GnomAD database, including 19,880 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 (19880 hom., cov: 32)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76
• Publications: 3 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.209+24046T>C		intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2	n.81-98282T>C		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.209+24046T>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+24046T>C		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745512.1	n.341+24046T>C		intron_variant	Intron 2 of 5
ENSG00000228944	ENST00000745513.1	n.309+24046T>C		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745514.1	n.328+24046T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76898 AN: 151948 Hom.: 19870 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.673

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: 76946 AN: 152066 Hom.: 19880 Cov.: 32 AF XY: 0.510 AC XY: 37936 AN XY: 74330

African (AFR) AF: 0.421 AC: 17475 AN: 41468

American (AMR) AF: 0.619 AC: 9463 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1913 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3481 AN: 5174

South Asian (SAS) AF: 0.540 AC: 2602 AN: 4816

European-Finnish (FIN) AF: 0.517 AC: 5458 AN: 10556

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

European-Non Finnish (NFE) AF: 0.514 AC: 34920 AN: 67980

Other (OTH) AF: 0.509 AC: 1072 AN: 2106

Alfa AF: 0.518 Hom.: 4260

Bravo AF: 0.510

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	-1.0
CADD	Benign	0.019
DANN	Benign	0.27
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs16119; hg19: chr7-24334930;