rs4752485

Positions:

• chr10-120961461-C-T

Variant summary

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

The ENST00000414774.1(ENSG00000227307):​n.49+19191G>A 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 0.72 in 151,970 control chromosomes in the GnomAD database, including 39,368 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 0.72 (39368 hom., cov: 33)
• Consequence: ENST00000414774.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378519	XR_001747609.2	n.540+19191G>A		intron_variant, non_coding_transcript_variant
LOC105378519	XR_946372.3	n.73+19191G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000414774.1	n.49+19191G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109301 AN: 151854 Hom.: 39348 Cov.: 33

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.635

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.720 AC: 109380 AN: 151970 Hom.: 39368 Cov.: 33 AF XY: 0.719 AC XY: 53427 AN XY: 74282

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.694

Alfa AF: 0.728 Hom.: 39225

Bravo AF: 0.721

Asia WGS AF: 0.705 AC: 2439 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4752485; hg19: chr10-122720974;