4-104309490-A-C

Variant names:

• chr4-104309490-A-C
• rs960345
• ENST00000505680.1:n.57-21912A>C

Variant summary

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

The ENST00000505680.1(ENSG00000251170):​n.57-21912A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,008 control chromosomes in the GnomAD database, including 17,172 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 0.45 (17172 hom., cov: 33)
• Consequence: ENSG00000251170 ENST00000505680.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 3 publications found

Genes affected

ENSG00000251170 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377350	XR_939033.3	n.236-25999T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251170	ENST00000505680.1	n.57-21912A>C		intron_variant	Intron 1 of 3	3
ENSG00000251170	ENST00000514327.5	n.163-22733A>C		intron_variant	Intron 2 of 5	4
ENSG00000302240	ENST00000785137.1	n.236-25999T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68926 AN: 151890 Hom.: 17159 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.454 AC: 68961 AN: 152008 Hom.: 17172 Cov.: 33 AF XY: 0.458 AC XY: 34047 AN XY: 74272

African (AFR) AF: 0.262 AC: 10878 AN: 41496

American (AMR) AF: 0.572 AC: 8719 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3470

East Asian (EAS) AF: 0.812 AC: 4196 AN: 5168

South Asian (SAS) AF: 0.608 AC: 2937 AN: 4832

European-Finnish (FIN) AF: 0.437 AC: 4609 AN: 10536

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34238 AN: 67942

Other (OTH) AF: 0.480 AC: 1012 AN: 2108

Alfa AF: 0.503 Hom.: 9288

Bravo AF: 0.457

Asia WGS AF: 0.662 AC: 2302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs960345; hg19: chr4-105230647;