rs10489707

Positions:

• chr1-185659752-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.1067-19697A>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 0.0741 in 152,302 control chromosomes in the GnomAD database, including 1,097 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 0.074 (1097 hom., cov: 32)
• Consequence: LOC107985239 XR_001738340.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564

Genes affected

LOC107985239 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985239	XR_001738340.2	n.1067-19697A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0739 AC: 11242 AN: 152184 Hom.: 1085 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.0471

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0102

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.00910

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0741 AC: 11285 AN: 152302 Hom.: 1097 Cov.: 32 AF XY: 0.0713 AC XY: 5312 AN XY: 74478

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.0363

Gnomad4 ASJ AF: 0.0562

Gnomad4 EAS AF: 0.0474

Gnomad4 SAS AF: 0.0373

Gnomad4 FIN AF: 0.0102

Gnomad4 NFE AF: 0.00907

Gnomad4 OTH AF: 0.0704

Alfa AF: 0.0294 Hom.: 138

Bravo AF: 0.0857

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489707; hg19: chr1-185628884;