rs13414052

chr2-219986453-G-A

Variant summary

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

The ENST00000702748.1(ENSG00000288902):n.312-38180G>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 0.244 in 152,112 control chromosomes in the GnomAD database, including 5,377 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 0.24 (5377 hom., cov: 32)
• Consequence: ENST00000702748.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373891	XR_001739888.2	n.304-27317G>A		intron_variant, non_coding_transcript_variant
LOC105373891	XR_923928.3	n.124+25670G>A		intron_variant, non_coding_transcript_variant
LOC105373891	XR_923930.3	n.124+25670G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000702748.1	n.312-38180G>A		intron_variant, non_coding_transcript_variant
	ENST00000692185.1	n.279-38180G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37121 AN: 151994 Hom.: 5378 Cov.: 32

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.244 AC: 37135 AN: 152112 Hom.: 5377 Cov.: 32 AF XY: 0.247 AC XY: 18354 AN XY: 74362

Gnomad4 AFR AF: 0.0887

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.259

Alfa AF: 0.303 Hom.: 7636

Bravo AF: 0.225

Asia WGS AF: 0.277 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.039
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13414052; hg19: chr2-220851174;