rs4751808

chr10-120917550-A-G

Variant summary

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

The XR_001747609.2(LOC105378519):n.541-15208T>C 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 0.651 in 152,180 control chromosomes in the GnomAD database, including 33,105 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 0.65 (33105 hom., cov: 34)
• Consequence: LOC105378519 XR_001747609.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

Genes affected

LOC105378519 (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 = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378519	XR_001747609.2	n.541-15208T>C		intron_variant, non_coding_transcript_variant
LOC105378519	XR_946372.3	n.226+8738T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98914 AN: 152060 Hom.: 33050 Cov.: 34

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.651 AC: 99023 AN: 152180 Hom.: 33105 Cov.: 34 AF XY: 0.643 AC XY: 47810 AN XY: 74396

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.647

Alfa AF: 0.602 Hom.: 48467

Bravo AF: 0.668

Asia WGS AF: 0.560 AC: 1949 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	2.9
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4751808; hg19: chr10-122677062;