1-39829228-T-C

Variant names:

• chr1-39829228-T-C
• rs2172362
• ENST00000780948.1:n.218+3525T>C

Variant summary

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

The ENST00000780948.1(ENSG00000301696):​n.218+3525T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,044 control chromosomes in the GnomAD database, including 27,375 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 0.58 (27375 hom., cov: 32)
• Consequence: ENSG00000301696 ENST00000780948.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395
• Publications: 4 publications found

Genes affected

ENSG00000301696 (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 = 0.826 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780948.1. 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
	ENSG00000301696	ENST00000780948.1		n.218+3525T>C		intron	N/A
	ENSG00000301696	ENST00000780949.1		n.191-2743T>C		intron	N/A
	ENSG00000301696	ENST00000780950.1		n.174+3525T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87737 AN: 151926 Hom.: 27313 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.578 AC: 87854 AN: 152044 Hom.: 27375 Cov.: 32 AF XY: 0.575 AC XY: 42698 AN XY: 74290

African (AFR) AF: 0.834 AC: 34579 AN: 41480

American (AMR) AF: 0.496 AC: 7577 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1915 AN: 3468

East Asian (EAS) AF: 0.603 AC: 3118 AN: 5170

South Asian (SAS) AF: 0.498 AC: 2398 AN: 4812

European-Finnish (FIN) AF: 0.481 AC: 5072 AN: 10552

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31694 AN: 67962

Other (OTH) AF: 0.526 AC: 1112 AN: 2114

Alfa AF: 0.535 Hom.: 2841

Bravo AF: 0.591

Asia WGS AF: 0.602 AC: 2092 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	8.9
DANN	Benign	0.51
PhyloP100		0.40

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: rs2172362;

hg19: chr1-40294900;