rs7477069

chr10-52782378-G-Achr10-52782378-G-Cchr10-52782378-G-T

Variant summary

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

The XR_945965.3(LOC105378307):n.749C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,828 control chromosomes in the GnomAD database, including 8,429 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 0.33 (8429 hom., cov: 31)
• Consequence: LOC105378307 XR_945965.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

Genes affected

LOC105378307 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378307	XR_945965.3	n.749C>T		non_coding_transcript_exon_variant	4/4
LOC105378306	XR_945963.2	n.386+2835G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49393 AN: 151710 Hom.: 8430 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.325 AC: 49401 AN: 151828 Hom.: 8429 Cov.: 31 AF XY: 0.326 AC XY: 24172 AN XY: 74190

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.338

Alfa AF: 0.358 Hom.: 16003

Bravo AF: 0.321

Asia WGS AF: 0.355 AC: 1234 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	0.032
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7477069; hg19: chr10-54542138;