rs10489712

chr1-185678060-A-G

Variant summary

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

The XR_001738340.2(LOC107985239):n.1067-1389A>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 0.0662 in 152,210 control chromosomes in the GnomAD database, including 882 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 0.066 (882 hom., cov: 32)
• Consequence: LOC107985239 XR_001738340.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

LOC107985239 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985239	XR_001738340.2	n.1067-1389A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0659 AC: 10028 AN: 152092 Hom.: 870 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.0102

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00797

Gnomad OTH AF: 0.0640

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

GnomAD4 genome AF: 0.0662 AC: 10071 AN: 152210 Hom.: 882 Cov.: 32 AF XY: 0.0638 AC XY: 4746 AN XY: 74416

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.0322

Gnomad4 ASJ AF: 0.0501

Gnomad4 EAS AF: 0.0469

Gnomad4 SAS AF: 0.0329

Gnomad4 FIN AF: 0.0102

Gnomad4 NFE AF: 0.00794

Gnomad4 OTH AF: 0.0633

Alfa AF: 0.0383 Hom.: 108

Bravo AF: 0.0762

Asia WGS AF: 0.0710 AC: 246 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.1
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489712; hg19: chr1-185647192;