rs2900032

chr14-48468728-T-C

Variant summary

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

The ENST00000555693.1(ENSG00000258751):n.123+22917A>G 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 0.0629 in 151,526 control chromosomes in the GnomAD database, including 351 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 0.063 (351 hom., cov: 32)
• Consequence: ENST00000555693.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

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 = 0.072 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378178	XR_007064152.1	n.426-39485A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000555693.1	n.123+22917A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0630 AC: 9536 AN: 151408 Hom.: 351 Cov.: 32

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.0720

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

GnomAD4 genome AF: 0.0629 AC: 9537 AN: 151526 Hom.: 351 Cov.: 32 AF XY: 0.0624 AC XY: 4622 AN XY: 74074

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.0503

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0567

Gnomad4 FIN AF: 0.0925

Gnomad4 NFE AF: 0.0737

Gnomad4 OTH AF: 0.0712

Alfa AF: 0.0648 Hom.: 43

Bravo AF: 0.0582

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.6
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2900032; hg19: chr14-48937931;