rs4948674

Variant names:

• chr10-45450242-C-A
• rs4948674
• ENST00000435635.1:n.179+2602G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-45450242-C-A
• chr10-45450242-C-G
• chr10-45450242-C-T

Variant summary

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

The ENST00000435635.1(ENSG00000231964):​n.179+2602G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,094 control chromosomes in the GnomAD database, including 9,948 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 0.36 (9948 hom., cov: 32)
• Consequence: ENSG00000231964 ENST00000435635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 8 publications found

Genes affected

ENSG00000231964 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435635.1. 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
	LOC102724323	NR_120674.1		n.179+2602G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231964	ENST00000435635.1	TSL:2	n.179+2602G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54168 AN: 151976 Hom.: 9943 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.356 AC: 54211 AN: 152094 Hom.: 9948 Cov.: 32 AF XY: 0.349 AC XY: 25940 AN XY: 74358

African (AFR) AF: 0.313 AC: 12969 AN: 41482

American (AMR) AF: 0.367 AC: 5621 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3470

East Asian (EAS) AF: 0.159 AC: 822 AN: 5176

South Asian (SAS) AF: 0.216 AC: 1041 AN: 4830

European-Finnish (FIN) AF: 0.394 AC: 4157 AN: 10560

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27025 AN: 67962

Other (OTH) AF: 0.363 AC: 767 AN: 2114

Alfa AF: 0.300 Hom.: 1247

Bravo AF: 0.354

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.60
PhyloP100		0.14

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: rs4948674;

hg19: chr10-45945690;