1-183470348-C-T

Position:

• chr1-183470348-C-T

Variant summary

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

The NR_040063.1(SMG7-AS1):​n.1339+117G>A 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 0.65 in 152,178 control chromosomes in the GnomAD database, including 32,362 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 0.65 (32362 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: SMG7-AS1 NR_040063.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

Genes affected

SMG7-AS1 (HGNC:24518): (SMG7 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMG7-AS1	NR_040063.1	n.1339+117G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMG7-AS1	ENST00000421703.5	n.1103+117G>A		intron_variant, non_coding_transcript_variant		1
SMG7-AS1	ENST00000624060.2	n.2549G>A		non_coding_transcript_exon_variant	1/1
SMG7-AS1	ENST00000432837.1	n.246+117G>A		intron_variant, non_coding_transcript_variant		3
SMG7-AS1	ENST00000663067.1	n.271+117G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98861 AN: 152058 Hom.: 32335 Cov.: 33

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.645

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.650 AC: 98931 AN: 152176 Hom.: 32362 Cov.: 33 AF XY: 0.647 AC XY: 48113 AN XY: 74396

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.643

Alfa AF: 0.634 Hom.: 50711

Bravo AF: 0.649

Asia WGS AF: 0.523 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.0
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2275675; hg19: chr1-183439483;