ENST00000625056.3:n.241+245C>T

Variant names:

• chr16-84924412-G-A
• rs7188498
• ENST00000625056.3:n.241+245C>T

Variant summary

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

The ENST00000625056.3(ENSG00000279622):​n.241+245C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,054 control chromosomes in the GnomAD database, including 7,306 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 0.30 (7306 hom., cov: 34)
• Consequence: ENSG00000279622 ENST00000625056.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 3 publications found

Genes affected

ENSG00000279622 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279622	ENST00000625056.3	n.241+245C>T		intron_variant	Intron 1 of 2	6
ENSG00000279622	ENST00000741212.1	n.131+367C>T		intron_variant	Intron 1 of 2
ENSG00000279622	ENST00000741213.1	n.115+367C>T		intron_variant	Intron 1 of 2
ENSG00000279622	ENST00000741214.1	n.157+367C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45114 AN: 151936 Hom.: 7299 Cov.: 34

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.297 AC: 45160 AN: 152054 Hom.: 7306 Cov.: 34 AF XY: 0.296 AC XY: 22022 AN XY: 74332

African (AFR) AF: 0.438 AC: 18152 AN: 41444

American (AMR) AF: 0.308 AC: 4704 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3470

East Asian (EAS) AF: 0.187 AC: 966 AN: 5156

South Asian (SAS) AF: 0.191 AC: 921 AN: 4828

European-Finnish (FIN) AF: 0.235 AC: 2484 AN: 10590

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.237 AC: 16123 AN: 67960

Other (OTH) AF: 0.291 AC: 615 AN: 2110

Alfa AF: 0.255 Hom.: 23362

Bravo AF: 0.308

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.51
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7188498; hg19: chr16-84958018;