rs10799541

Positions:

• chr1-224223894-G-A
• chr1-224223894-G-C

Variant summary

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

The NR_110668.1(LOC101927164):​n.705+66G>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 0.348 in 152,000 control chromosomes in the GnomAD database, including 9,373 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 0.35 (9372 hom., cov: 31)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: LOC101927164 NR_110668.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927164	NR_110668.1	n.705+66G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000420350.1	n.705+66G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52837 AN: 151876 Hom.: 9371 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.353

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 1 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.348 AC: 52859 AN: 151994 Hom.: 9372 Cov.: 31 AF XY: 0.351 AC XY: 26057 AN XY: 74282

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.356

Alfa AF: 0.339 Hom.: 17814

Bravo AF: 0.353

Asia WGS AF: 0.426 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.71
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10799541; hg19: chr1-224411596;