rs10762885

Positions:

• chr10-52785830-G-A

Variant summary

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

The XR_945963.2(LOC105378306):​n.387-4368G>A 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 0.569 in 151,668 control chromosomes in the GnomAD database, including 25,548 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 0.57 (25548 hom., cov: 31)
• Consequence: LOC105378306 XR_945963.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01

Genes affected

LOC105378306 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378306	XR_945963.2	n.387-4368G>A		intron_variant, non_coding_transcript_variant
LOC105378307	XR_945965.3	n.370-1496C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86246 AN: 151552 Hom.: 25530 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.569 AC: 86312 AN: 151668 Hom.: 25548 Cov.: 31 AF XY: 0.572 AC XY: 42410 AN XY: 74112

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.582

Alfa AF: 0.609 Hom.: 52929

Bravo AF: 0.577

Asia WGS AF: 0.700 AC: 2434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.086
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10762885; hg19: chr10-54545590;