rs10456831

chr6-18506533-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_926549.3(LOC105374955):n.290-2339C>T 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 0.0344 in 152,258 control chromosomes in the GnomAD database, including 101 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 0.034 (101 hom., cov: 32)
• Consequence: LOC105374955 XR_926549.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

Genes affected

LOC105374955 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0344 (5239/152258) while in subpopulation NFE AF= 0.0448 (3046/68018). AF 95% confidence interval is 0.0435. There are 101 homozygotes in gnomad4. There are 2550 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 101 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374955	XR_926549.3	n.290-2339C>T		intron_variant, non_coding_transcript_variant
LOC105374955	XR_926548.3	n.273-2339C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0345 AC: 5242 AN: 152140 Hom.: 101 Cov.: 32

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0448

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0344 AC: 5239 AN: 152258 Hom.: 101 Cov.: 32 AF XY: 0.0343 AC XY: 2550 AN XY: 74442

Gnomad4 AFR AF: 0.0171

Gnomad4 AMR AF: 0.0429

Gnomad4 ASJ AF: 0.0423

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0342

Gnomad4 FIN AF: 0.0376

Gnomad4 NFE AF: 0.0448

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0392 Hom.: 10

Bravo AF: 0.0338

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	3.5
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10456831; hg19: chr6-18506764;