7-24224894-T-G

Variant names:

• chr7-24224894-T-G
• rs16213
• ENST00000439839.1:n.160-27865A>C

Variant summary

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

The ENST00000439839.1(ENSG00000228944):​n.160-27865A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,982 control chromosomes in the GnomAD database, including 20,291 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 0.50 (20291 hom., cov: 32)
• Consequence: ENSG00000228944 ENST00000439839.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.210-27865A>C		intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2	n.81-27865A>C		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.210-27865A>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228944	ENST00000439839.1	n.160-27865A>C		intron_variant	Intron 1 of 1	5
ENSG00000228944	ENST00000718234.1	n.320-27865A>C		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745512.1	n.342-27865A>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75890 AN: 151864 Hom.: 20260 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.500 AC: 75974 AN: 151982 Hom.: 20291 Cov.: 32 AF XY: 0.501 AC XY: 37215 AN XY: 74294

African (AFR) AF: 0.695 AC: 28816 AN: 41442

American (AMR) AF: 0.495 AC: 7558 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1587 AN: 3472

East Asian (EAS) AF: 0.615 AC: 3166 AN: 5150

South Asian (SAS) AF: 0.490 AC: 2354 AN: 4802

European-Finnish (FIN) AF: 0.413 AC: 4357 AN: 10552

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26597 AN: 67964

Other (OTH) AF: 0.504 AC: 1064 AN: 2110

Alfa AF: 0.428 Hom.: 61631

Bravo AF: 0.516

Asia WGS AF: 0.572 AC: 1987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.0
DANN	Benign	0.31
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs16213; hg19: chr7-24264513;