rs2009658

Positions:

• chr6-31570467-C-G

Variant summary

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

The NR_149045.1(LOC100287329):​n.121+2116G>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 0.147 in 152,206 control chromosomes in the GnomAD database, including 1,725 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 (1725 hom., cov: 32)
• Consequence: LOC100287329 NR_149045.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

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 (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100287329	NR_149045.1	n.121+2116G>C		intron_variant, non_coding_transcript_variant
LTA	XM_047418773.1	c.-341-1025C>G		intron_variant			XP_047274729.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000691266.1	n.118+2116G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22338 AN: 152088 Hom.: 1727 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.147 AC: 22346 AN: 152206 Hom.: 1725 Cov.: 32 AF XY: 0.148 AC XY: 11022 AN XY: 74428

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.163

Alfa AF: 0.155 Hom.: 1100

Bravo AF: 0.144

Asia WGS AF: 0.222 AC: 773 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	1.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2009658; hg19: chr6-31538244;