rs10490848

Positions:

• chr3-144330979-A-G

Variant summary

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

The XR_007096124.1(LOC105374140):​n.20072+26175A>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 0.0333 in 152,304 control chromosomes in the GnomAD database, including 235 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 0.033 (235 hom., cov: 32)
• Consequence: LOC105374140 XR_007096124.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

Genes affected

LOC105374140 (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 (AFR) allele frequency at 95% confidence interval = 0.0965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374140	XR_007096124.1	n.20072+26175A>G		intron_variant, non_coding_transcript_variant
LOC105374140	XR_001740941.2	n.20090+60630A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0332 AC: 5052 AN: 152186 Hom.: 227 Cov.: 32

Gnomad AFR AF: 0.0987

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0122

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0379

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0189

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00369

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0333 AC: 5078 AN: 152304 Hom.: 235 Cov.: 32 AF XY: 0.0331 AC XY: 2467 AN XY: 74476

Gnomad4 AFR AF: 0.0991

Gnomad4 AMR AF: 0.0122

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0386

Gnomad4 SAS AF: 0.0141

Gnomad4 FIN AF: 0.0189

Gnomad4 NFE AF: 0.00369

Gnomad4 OTH AF: 0.0251

Alfa AF: 0.00796 Hom.: 28

Bravo AF: 0.0355

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490848; hg19: chr3-144049821;