rs4933466

Positions:

• chr10-88089762-A-G
• chr10-88089762-A-T

Variant summary

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

The XR_007062225.1(LOC105378415):​n.82-20T>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 0.356 in 152,222 control chromosomes in the GnomAD database, including 10,898 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 0.36 (10898 hom., cov: 33)
• Consequence: LOC105378415 XR_007062225.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

Genes affected

LOC105378415 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378415	XR_007062225.1	n.82-20T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54239 AN: 152104 Hom.: 10893 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.356 AC: 54260 AN: 152222 Hom.: 10898 Cov.: 33 AF XY: 0.363 AC XY: 27045 AN XY: 74414

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.357

Alfa AF: 0.386 Hom.: 15563

Bravo AF: 0.350

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.13
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4933466; hg19: chr10-89849519;