rs2071590

chr6-31571991-A-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+592T>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 0.687 in 154,080 control chromosomes in the GnomAD database, including 36,601 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 0.69 (36050 hom., cov: 30)
  • Exomes 𝑓: 0.69 (551 hom.)
• Consequence: LOC100287329 NR_149045.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100287329	NR_149045.1	n.121+592T>C		intron_variant, non_coding_transcript_variant
LTA	XM_047418773.1	c.-177-144A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691266.1	n.118+592T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104168 AN: 151622 Hom.: 36007 Cov.: 30

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.687

GnomAD4 exome AF: 0.688 AC: 1610 AN: 2340 Hom.: 551 AF XY: 0.695 AC XY: 955 AN XY: 1374

Gnomad4 AFR exome AF: 0.821

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.667

Gnomad4 EAS exome AF: 0.667

Gnomad4 SAS exome AF: 0.650

Gnomad4 FIN exome AF: 0.710

Gnomad4 NFE exome AF: 0.626

Gnomad4 OTH exome AF: 0.726

GnomAD4 genome AF: 0.687 AC: 104266 AN: 151740 Hom.: 36050 Cov.: 30 AF XY: 0.692 AC XY: 51316 AN XY: 74136

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.685

Alfa AF: 0.605 Hom.: 12859

Bravo AF: 0.678

Asia WGS AF: 0.725 AC: 2522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.5
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2071590; hg19: chr6-31539768;