rs2441010

Variant names:

• chr5-83389441-C-T
• rs2441010
• ENST00000823088.1:n.225+1072C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000823088.1(ENSG00000307051):​n.225+1072C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 151,990 control chromosomes in the GnomAD database, including 495 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 0.073 (495 hom., cov: 32)
• Consequence: ENSG00000307051 ENST00000823088.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.774
• Publications: 2 publications found

Genes affected

ENSG00000307051 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000823088.1. 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
	ENSG00000307051	ENST00000823088.1		n.225+1072C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0728 AC: 11049 AN: 151872 Hom.: 495 Cov.: 32

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0725

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0932

Gnomad OTH AF: 0.0696

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

GnomAD4 genome AF: 0.0727 AC: 11051 AN: 151990 Hom.: 495 Cov.: 32 AF XY: 0.0731 AC XY: 5432 AN XY: 74284

African (AFR) AF: 0.0186 AC: 772 AN: 41530

American (AMR) AF: 0.0805 AC: 1227 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3468

East Asian (EAS) AF: 0.0727 AC: 377 AN: 5186

South Asian (SAS) AF: 0.108 AC: 519 AN: 4822

European-Finnish (FIN) AF: 0.111 AC: 1173 AN: 10570

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0932 AC: 6324 AN: 67856

Other (OTH) AF: 0.0703 AC: 148 AN: 2104

Alfa AF: 0.0889 Hom.: 924

Bravo AF: 0.0675

Asia WGS AF: 0.106 AC: 369 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
CADD	Benign	19
DANN	Benign	0.63
PhyloP100		0.77

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: rs2441010;

hg19: chr5-82685260;