chr1-39829228-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378667	XR_947221.3	n.429-2743T>C		intron_variant	Intron 2 of 3
LOC105378667	XR_947222.3	n.173-2743T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301696	ENST00000780948.1	n.218+3525T>C		intron_variant	Intron 2 of 2
ENSG00000301696	ENST00000780949.1	n.191-2743T>C		intron_variant	Intron 2 of 3
ENSG00000301696	ENST00000780950.1	n.174+3525T>C		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs2172362; hg19: chr1-40294900;