rs4835147

Variant names:

• chr4-148918760-C-A
• rs4835147
• ENST00000661928.1:n.347+51879C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-148918760-C-A
• chr4-148918760-C-G
• chr4-148918760-C-T

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.347+51879C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,876 control chromosomes in the GnomAD database, including 10,090 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 0.35 (10090 hom., cov: 32)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.14
• Publications: 3 publications found

Genes affected

ENSG00000287292 (HGNC:58892):

LOC107986195 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661928.1. 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
	ENSG00000287292	ENST00000661928.1		n.347+51879C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52541 AN: 151758 Hom.: 10078 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.346 AC: 52601 AN: 151876 Hom.: 10090 Cov.: 32 AF XY: 0.342 AC XY: 25405 AN XY: 74248

African (AFR) AF: 0.520 AC: 21515 AN: 41404

American (AMR) AF: 0.366 AC: 5586 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1126 AN: 3468

East Asian (EAS) AF: 0.372 AC: 1917 AN: 5148

South Asian (SAS) AF: 0.259 AC: 1247 AN: 4816

European-Finnish (FIN) AF: 0.176 AC: 1858 AN: 10558

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18400 AN: 67910

Other (OTH) AF: 0.326 AC: 687 AN: 2106

Alfa AF: 0.287 Hom.: 3445

Bravo AF: 0.370

Asia WGS AF: 0.318 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.022
DANN	Benign	0.49
PhyloP100		-4.1

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: rs4835147;

hg19: chr4-149839912;