rs9321637

chr6-137945548-T-C

Variant summary

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

The NR_149097.1(SIMALR):n.132+121A>G 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 0.166 in 152,388 control chromosomes in the GnomAD database, including 2,777 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 0.17 (2776 hom., cov: 31)
  • Exomes 𝑓: 0.076 (1 hom.)
• Consequence: SIMALR NR_149097.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

LINC02865 (HGNC:54516): (long intergenic non-protein coding RNA 2865)

SIMALR (HGNC:53554): (suppressor of inflammatory macrophage apoptosis lncRNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SIMALR	NR_149097.1	n.132+121A>G		intron_variant, non_coding_transcript_variant
LINC02865	NR_174953.1	n.119+82T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02865	ENST00000417800.1	n.101+82T>C		intron_variant, non_coding_transcript_variant		2
SIMALR	ENST00000689325.1	n.230+121A>G		intron_variant, non_coding_transcript_variant
SIMALR	ENST00000417932.1	n.134+121A>G		intron_variant, non_coding_transcript_variant		3
LINC02865	ENST00000434437.5	n.101+82T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25208 AN: 152086 Hom.: 2776 Cov.: 31

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.0761 AC: 14 AN: 184 Hom.: 1 Cov.: 0 AF XY: 0.0556 AC XY: 6 AN XY: 108

Gnomad4 EAS exome AF: 0.0580

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.136

GnomAD4 genome AF: 0.166 AC: 25221 AN: 152204 Hom.: 2776 Cov.: 31 AF XY: 0.162 AC XY: 12071 AN XY: 74412

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.0942

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0235

Gnomad4 SAS AF: 0.0783

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.144

Alfa AF: 0.124 Hom.: 1977

Bravo AF: 0.168

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.2
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321637; hg19: chr6-138266685;