17-31048159-A-G

Position:

• chr17-31048159-A-G

Variant summary

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

The NR_146737.1(LOC646030):​n.464-2878T>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 0.196 in 152,172 control chromosomes in the GnomAD database, including 8,886 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 0.20 (8886 hom., cov: 32)
• Consequence: LOC646030 NR_146737.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC646030	NR_146737.1	n.464-2878T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000579164.6	n.1140-452T>C		intron_variant, non_coding_transcript_variant
	ENST00000580053.1	n.143+2610A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000581652.1	n.194-2878T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29734 AN: 152054 Hom.: 8858 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0832

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0400

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.196 AC: 29811 AN: 152172 Hom.: 8886 Cov.: 32 AF XY: 0.191 AC XY: 14184 AN XY: 74410

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.0829

Gnomad4 ASJ AF: 0.0234

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0390

Gnomad4 FIN AF: 0.0166

Gnomad4 NFE AF: 0.0138

Gnomad4 OTH AF: 0.153

Alfa AF: 0.148 Hom.: 867

Bravo AF: 0.219

Asia WGS AF: 0.0550 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
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: rs6505228; hg19: chr17-29375177;