rs1227244

Positions:

• chr10-64831068-A-G

Variant summary

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

The XR_946020.2(LOC105378336):​n.49+16066A>G 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 151,694 control chromosomes in the GnomAD database, including 9,823 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 (9823 hom., cov: 32)
• Consequence: LOC105378336 XR_946020.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

LOC105378336 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378336	XR_946020.2	n.49+16066A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.356 AC: 53971 AN: 151576 Hom.: 9810 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.356 AC: 54013 AN: 151694 Hom.: 9823 Cov.: 32 AF XY: 0.357 AC XY: 26460 AN XY: 74144

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.350

Alfa AF: 0.343 Hom.: 2104

Bravo AF: 0.347

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1227244; hg19: chr10-66590825;