rs1817567

chr2-183933099-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441026.1(ENSG00000234172):n.104-1274G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 150,420 control chromosomes in the GnomAD database, including 3,747 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 0.18 (3747 hom., cov: 31)
• Consequence: ENST00000441026.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000441026.1	n.104-1274G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.178 AC: 26776 AN: 150312 Hom.: 3749 Cov.: 31

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.0582

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.178 AC: 26771 AN: 150420 Hom.: 3747 Cov.: 31 AF XY: 0.172 AC XY: 12633 AN XY: 73300

Gnomad4 AFR AF: 0.0636

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.0581

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.169

Alfa AF: 0.237 Hom.: 5601

Bravo AF: 0.166

Asia WGS AF: 0.0980 AC: 339 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.26
Dann	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1817567; hg19: chr2-184797826;