rs798443

chr2-7828144-G-Achr2-7828144-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_922750.1(LOC105373408):n.274+212C>T variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.614 in 151,978 control chromosomes in the GnomAD database, including 34,578 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 0.61 (34578 hom., cov: 31)
• Consequence: LOC105373408 XR_922750.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.18

Genes affected

LOC105373408 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373408	XR_922750.1	n.274+212C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93339 AN: 151858 Hom.: 34568 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.614 AC: 93355 AN: 151978 Hom.: 34578 Cov.: 31 AF XY: 0.618 AC XY: 45917 AN XY: 74292

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.621

Alfa AF: 0.767 Hom.: 95389

Bravo AF: 0.582

Asia WGS AF: 0.642 AC: 2231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
Cadd	Benign	15
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs798443; hg19: chr2-7968275;