rs10002492

Positions:

• chr4-12578222-A-G

Variant summary

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

The XR_001741374.1(LOC105374492):​n.254+44433T>C 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 0.215 in 152,048 control chromosomes in the GnomAD database, including 5,119 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 0.21 (5119 hom., cov: 32)
• Consequence: LOC105374492 XR_001741374.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

LOC105374492 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374492	XR_001741374.1	n.254+44433T>C		intron_variant, non_coding_transcript_variant
LOC105374492	XR_925406.4	n.477+31120T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32599 AN: 151932 Hom.: 5097 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.215 AC: 32659 AN: 152048 Hom.: 5119 Cov.: 32 AF XY: 0.209 AC XY: 15547 AN XY: 74298

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0282

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.190

Alfa AF: 0.178 Hom.: 626

Bravo AF: 0.223

Asia WGS AF: 0.0980 AC: 341 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10002492; hg19: chr4-12579846;