rs2172362

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-39829228-T-A
• chr1-39829228-T-C
• chr1-39829228-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000780948.1(ENSG00000301696):​n.218+3525T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378667	XR_947221.3	n.429-2743T>A		intron_variant	Intron 2 of 3
LOC105378667	XR_947222.3	n.173-2743T>A		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>A		intron_variant	Intron 2 of 2
ENSG00000301696	ENST00000780949.1	n.191-2743T>A		intron_variant	Intron 2 of 3
ENSG00000301696	ENST00000780950.1	n.174+3525T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.5
DANN	Benign	0.56
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;