rs10494904

chr1-208709976-G-C

Variant summary

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

The XR_007066854.1(LOC105372892):n.159+17965C>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 0.144 in 152,138 control chromosomes in the GnomAD database, including 3,798 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 0.14 (3798 hom., cov: 32)
• Consequence: LOC105372892 XR_007066854.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

Genes affected

LOC105372892 (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 (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372892	XR_007066854.1	n.159+17965C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21795 AN: 152020 Hom.: 3779 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.0485

Gnomad FIN AF: 0.0561

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0223

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.144 AC: 21860 AN: 152138 Hom.: 3798 Cov.: 32 AF XY: 0.142 AC XY: 10584 AN XY: 74366

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.0860

Gnomad4 ASJ AF: 0.0757

Gnomad4 EAS AF: 0.0663

Gnomad4 SAS AF: 0.0483

Gnomad4 FIN AF: 0.0561

Gnomad4 NFE AF: 0.0223

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0963 Hom.: 298

Bravo AF: 0.160

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	8.0
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494904; hg19: chr1-208883321;