rs10841769

Variant names:

• chr12-21242085-G-A
• rs10841769
• XR_007063239.1:n.87-7786C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-21242085-G-A
• chr12-21242085-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007063239.1(LOC124902895):​n.87-7786C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,976 control chromosomes in the GnomAD database, including 17,123 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 0.47 (17123 hom., cov: 32)
• Consequence: LOC124902895 XR_007063239.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 4 publications found

Genes affected

LOC124902895 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902895	XR_007063239.1	n.87-7786C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71266 AN: 151858 Hom.: 17106 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.469 AC: 71327 AN: 151976 Hom.: 17123 Cov.: 32 AF XY: 0.474 AC XY: 35227 AN XY: 74256

African (AFR) AF: 0.428 AC: 17731 AN: 41444

American (AMR) AF: 0.444 AC: 6783 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1843 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3798 AN: 5156

South Asian (SAS) AF: 0.460 AC: 2212 AN: 4812

European-Finnish (FIN) AF: 0.520 AC: 5483 AN: 10552

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31678 AN: 67958

Other (OTH) AF: 0.480 AC: 1015 AN: 2116

Alfa AF: 0.462 Hom.: 24061

Bravo AF: 0.466

Asia WGS AF: 0.616 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs10841769; hg19: chr12-21395019;