rs4447485

Positions:

• chr17-78342606-C-T

Variant summary

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

The XR_935004.4(LOC105371912):​n.540C>T 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 0.149 in 152,424 control chromosomes in the GnomAD database, including 1,802 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 0.15 (1800 hom., cov: 32)
  • Exomes 𝑓: 0.13 (2 hom.)
• Consequence: LOC105371912 XR_935004.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390

Genes affected

LOC105371912 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371912	XR_935004.4	n.540C>T		non_coding_transcript_exon_variant	1/2
LOC105371912	XR_007065919.1	n.212+328C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000586321.1	n.61-1359C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22691 AN: 152064 Hom.: 1802 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.170

GnomAD4 exome AF: 0.128 AC: 31 AN: 242 Hom.: 2 AF XY: 0.139 AC XY: 25 AN XY: 180

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.200

Gnomad4 NFE exome AF: 0.137

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.149 AC: 22688 AN: 152182 Hom.: 1800 Cov.: 32 AF XY: 0.148 AC XY: 11044 AN XY: 74394

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.0929

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.169

Alfa AF: 0.164 Hom.: 2654

Bravo AF: 0.148

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.1
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4447485; hg19: chr17-76338687;