rs2146807

Positions:

• chr10-44318290-T-C

Variant summary

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

The XR_007062369.1(LOC124902544):​n.3743-20393A>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 0.162 in 152,208 control chromosomes in the GnomAD database, including 2,147 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 0.16 (2147 hom., cov: 32)
• Consequence: LOC124902544 XR_007062369.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

Genes affected

LOC124902544 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902544	XR_007062369.1	n.3743-20393A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24612 AN: 152090 Hom.: 2142 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0997

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0827

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.162 AC: 24642 AN: 152208 Hom.: 2147 Cov.: 32 AF XY: 0.163 AC XY: 12157 AN XY: 74434

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.0996

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.0827

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.161

Alfa AF: 0.142 Hom.: 1765

Bravo AF: 0.172

Asia WGS AF: 0.169 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
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: rs2146807; hg19: chr10-44813738;