rs2742624

Variant names:

• chr22-45280797-A-G
• rs2742624
• ENST00000781260.1:n.348+3684T>C

Variant summary

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

The ENST00000781260.1(ENSG00000301739):​n.348+3684T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,950 control chromosomes in the GnomAD database, including 26,195 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 0.55 (26195 hom., cov: 31)
• Consequence: ENSG00000301739 ENST00000781260.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667
• Publications: 14 publications found

Genes affected

ENSG00000301739 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000781260.1. 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
	ENSG00000301739	ENST00000781260.1		n.348+3684T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83322 AN: 151832 Hom.: 26207 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.548 AC: 83322 AN: 151950 Hom.: 26195 Cov.: 31 AF XY: 0.549 AC XY: 40722 AN XY: 74240

African (AFR) AF: 0.219 AC: 9092 AN: 41462

American (AMR) AF: 0.615 AC: 9364 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2530 AN: 3472

East Asian (EAS) AF: 0.472 AC: 2435 AN: 5162

South Asian (SAS) AF: 0.526 AC: 2534 AN: 4816

European-Finnish (FIN) AF: 0.680 AC: 7175 AN: 10546

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.708 AC: 48104 AN: 67948

Other (OTH) AF: 0.567 AC: 1195 AN: 2106

Alfa AF: 0.646 Hom.: 51733

Bravo AF: 0.530

Asia WGS AF: 0.462 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.3
DANN	Benign	0.76
PhyloP100		0.67

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: rs2742624;

hg19: chr22-45676678;