7-124117829-T-C

Variant names:

• chr7-124117829-T-C
• rs2215348
• ENST00000484322.5:n.168+68605T>C

Variant summary

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

The ENST00000484322.5(ENSG00000242593):​n.168+68605T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,972 control chromosomes in the GnomAD database, including 15,094 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 0.44 (15094 hom., cov: 32)
• Consequence: ENSG00000242593 ENST00000484322.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

Genes affected

ENSG00000242593 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 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
ENSG00000242593	ENST00000484322.5	n.168+68605T>C		intron_variant	Intron 2 of 8	1
ENSG00000242593	ENST00000650961.1	n.415+40457T>C		intron_variant	Intron 3 of 10
ENSG00000242593	ENST00000651674.1	n.93+68605T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66715 AN: 151854 Hom.: 15072 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.439 AC: 66788 AN: 151972 Hom.: 15094 Cov.: 32 AF XY: 0.440 AC XY: 32678 AN XY: 74262

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.445

Alfa AF: 0.403 Hom.: 24005

Bravo AF: 0.444

Asia WGS AF: 0.367 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.14
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2215348; hg19: chr7-123757883;