rs17439810

chr4-40043720-G-C

Variant summary

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

The NR_027277.2(LOC344967):n.810C>G 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 0.245 in 1,599,574 control chromosomes in the GnomAD database, including 50,963 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 0.21 (3773 hom., cov: 31)
  • Exomes 𝑓: 0.25 (47190 hom.)
• Consequence: LOC344967 NR_027277.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC344967	NR_027277.2	n.810C>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000381811.2	n.810C>G		non_coding_transcript_exon_variant	3/3	2
	ENST00000507914.2	n.416C>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31829 AN: 151914 Hom.: 3779 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.0569

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.264

GnomAD3 exomes AF: 0.215 AC: 54043 AN: 250842 Hom.: 6611 AF XY: 0.222 AC XY: 30151 AN XY: 135570

Gnomad AFR exome AF: 0.116

Gnomad AMR exome AF: 0.156

Gnomad ASJ exome AF: 0.327

Gnomad EAS exome AF: 0.0607

Gnomad SAS exome AF: 0.186

Gnomad FIN exome AF: 0.234

Gnomad NFE exome AF: 0.266

Gnomad OTH exome AF: 0.242

GnomAD4 exome AF: 0.249 AC: 360562 AN: 1447542 Hom.: 47190 Cov.: 31 AF XY: 0.249 AC XY: 179091 AN XY: 720542

Gnomad4 AFR exome AF: 0.112

Gnomad4 AMR exome AF: 0.161

Gnomad4 ASJ exome AF: 0.324

Gnomad4 EAS exome AF: 0.0604

Gnomad4 SAS exome AF: 0.185

Gnomad4 FIN exome AF: 0.232

Gnomad4 NFE exome AF: 0.267

Gnomad4 OTH exome AF: 0.253

GnomAD4 genome AF: 0.209 AC: 31816 AN: 152032 Hom.: 3773 Cov.: 31 AF XY: 0.206 AC XY: 15303 AN XY: 74304

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.0570

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.263

Alfa AF: 0.248 Hom.: 930

Bravo AF: 0.206

Asia WGS AF: 0.125 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	13
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17439810; hg19: chr4-40045340;