rs9904761

chr17-48879468-C-G

Variant summary

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

The NR_135674.1(LOC105371814):n.477-123G>C 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 0.329 in 152,046 control chromosomes in the GnomAD database, including 8,506 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 (8496 hom., cov: 31)
  • Exomes 𝑓: 0.29 (10 hom.)
• Consequence: LOC105371814 NR_135674.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371814	NR_135674.1	n.477-123G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000508743.1	n.477-123G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49895 AN: 151678 Hom.: 8479 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.333

GnomAD4 exome AF: 0.288 AC: 72 AN: 250 Hom.: 10 AF XY: 0.261 AC XY: 47 AN XY: 180

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.250

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.389

Gnomad4 NFE exome AF: 0.306

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.329 AC: 49960 AN: 151796 Hom.: 8496 Cov.: 31 AF XY: 0.330 AC XY: 24446 AN XY: 74188

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.332

Alfa AF: 0.325 Hom.: 1026

Bravo AF: 0.344

Asia WGS AF: 0.213 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	7.1
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9904761; hg19: chr17-46956830;