rs7188498

chr16-84924412-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000625056.2(ENSG00000279622):n.152+245C>T variant causes a intron, non coding transcript 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: ENST00000625056.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000625056.2	n.152+245C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.291

Alfa AF: 0.246 Hom.: 9869

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7188498; hg19: chr16-84958018;