7-24308272-G-T

Variant names:

• chr7-24308272-G-T
• rs16089
• ENST00000718234.1:n.319+11085C>A

Variant summary

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

The ENST00000718234.1(ENSG00000228944):​n.319+11085C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 148,774 control chromosomes in the GnomAD database, including 3,848 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 0.22 (3848 hom., cov: 28)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228944	ENST00000718234.1		n.319+11085C>A		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.341+11085C>A		intron	N/A
	ENSG00000228944	ENST00000745513.1		n.309+11085C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33131 AN: 148656 Hom.: 3846 Cov.: 28

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.223 AC: 33153 AN: 148774 Hom.: 3848 Cov.: 28 AF XY: 0.223 AC XY: 16102 AN XY: 72318

African (AFR) AF: 0.147 AC: 5943 AN: 40356

American (AMR) AF: 0.204 AC: 2947 AN: 14478

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 906 AN: 3452

East Asian (EAS) AF: 0.247 AC: 1236 AN: 5014

South Asian (SAS) AF: 0.363 AC: 1725 AN: 4756

European-Finnish (FIN) AF: 0.227 AC: 2241 AN: 9894

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17228 AN: 67572

Other (OTH) AF: 0.250 AC: 513 AN: 2050

Alfa AF: 0.239 Hom.: 16988

Bravo AF: 0.212

Asia WGS AF: 0.302 AC: 1050 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.92
DANN	Benign	0.35
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs16089; hg19: chr7-24347891;