rs4948674

Positions:

• chr10-45450242-C-A
• chr10-45450242-C-G
• chr10-45450242-C-T

Variant summary

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

The ENST00000435635.1(ENSG00000231964):​n.179+2602G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,094 control chromosomes in the GnomAD database, including 9,948 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 0.36 (9948 hom., cov: 32)
• Consequence: ENSG00000231964 ENST00000435635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

Genes affected

ENSG00000231964 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724323	NR_120674.1	n.179+2602G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231964	ENST00000435635.1	n.179+2602G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54168 AN: 151976 Hom.: 9943 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.356 AC: 54211 AN: 152094 Hom.: 9948 Cov.: 32 AF XY: 0.349 AC XY: 25940 AN XY: 74358

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.363

Alfa AF: 0.300 Hom.: 1247

Bravo AF: 0.354

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4948674; hg19: chr10-45945690;