rs10914386

Positions:

• chr1-31436225-A-C
• chr1-31436225-A-G

Variant summary

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

The XR_007065585.1(LOC124903900):​n.412-8616T>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 0.531 in 151,958 control chromosomes in the GnomAD database, including 25,273 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 0.53 (25273 hom., cov: 32)
• Consequence: LOC124903900 XR_007065585.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673

Genes affected

LOC124903900 (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 (NFE) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903900	XR_007065585.1	n.412-8616T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80685 AN: 151840 Hom.: 25278 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.531 AC: 80687 AN: 151958 Hom.: 25273 Cov.: 32 AF XY: 0.528 AC XY: 39242 AN XY: 74278

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.566

Alfa AF: 0.668 Hom.: 23991

Bravo AF: 0.510

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10914386; hg19: chr1-31909072;