rs960345

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-104309490-A-C
• chr4-104309490-A-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505680.1. 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
	ENSG00000251170	ENST00000505680.1	TSL:3	n.57-21912A>C		intron	N/A
	ENSG00000251170	ENST00000514327.5	TSL:4	n.163-22733A>C		intron	N/A
	ENSG00000302240	ENST00000785137.1		n.236-25999T>G		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs960345;

hg19: chr4-105230647;