rs954368

Positions:

• chr4-153850624-T-C

Variant summary

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

The variant allele was found at a frequency of 0.1 in 152,096 control chromosomes in the GnomAD database, including 935 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 0.10 (935 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.153850624T>C		intergenic_region
LOC101927947	XR_007058336.1	n.3440+8357T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15206 AN: 151978 Hom.: 931 Cov.: 31

Gnomad AFR AF: 0.0563

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.0819

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.100 AC: 15220 AN: 152096 Hom.: 935 Cov.: 31 AF XY: 0.101 AC XY: 7534 AN XY: 74360

Gnomad4 AFR AF: 0.0565

Gnomad4 AMR AF: 0.0580

Gnomad4 ASJ AF: 0.0819

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.0892

Alfa AF: 0.111 Hom.: 1432

Bravo AF: 0.0889

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs954368; hg19: chr4-154771776;