rs4752485

Variant names:

• chr10-120961461-C-T
• rs4752485
• ENST00000414774.1:n.49+19191G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414774.1(ENSG00000227307):​n.49+19191G>A variant causes a intron 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: ENSG00000227307 ENST00000414774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 5 publications found

Genes affected

ENSG00000227307 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414774.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227307	ENST00000414774.1	TSL:3	n.49+19191G>A		intron	N/A
	ENSG00000310027	ENST00000846644.1		n.*40C>T		downstream_gene	N/A

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

African (AFR) AF: 0.703 AC: 29135 AN: 41430

American (AMR) AF: 0.719 AC: 10982 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2249 AN: 3468

East Asian (EAS) AF: 0.732 AC: 3784 AN: 5168

South Asian (SAS) AF: 0.679 AC: 3272 AN: 4820

European-Finnish (FIN) AF: 0.715 AC: 7544 AN: 10548

Middle Eastern (MID) AF: 0.632 AC: 182 AN: 288

European-Non Finnish (NFE) AF: 0.735 AC: 49969 AN: 67960

Other (OTH) AF: 0.694 AC: 1464 AN: 2108

Alfa AF: 0.728 Hom.: 117050

Bravo AF: 0.721

Asia WGS AF: 0.705 AC: 2439 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.44

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4752485;

hg19: chr10-122720974;