1-183470348-C-T

Variant names:

• chr1-183470348-C-T
• rs2275675
• ENST00000421703.5:n.1103+117G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000773665.1(SMG7-AS1):​n.601G>A variant causes a non coding transcript exon 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 ENST00000773665.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 23 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773665.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMG7-AS1	NR_040063.1		n.1339+117G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMG7-AS1	ENST00000421703.5	TSL:1	n.1103+117G>A		intron	N/A
	SMG7-AS1	ENST00000624060.3	TSL:6	n.2549G>A		non_coding_transcript_exon	Exon 1 of 1
	SMG7-AS1	ENST00000773665.1		n.601G>A		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.729 AC: 30255 AN: 41514

American (AMR) AF: 0.598 AC: 9142 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2374 AN: 3472

East Asian (EAS) AF: 0.473 AC: 2448 AN: 5178

South Asian (SAS) AF: 0.592 AC: 2856 AN: 4828

European-Finnish (FIN) AF: 0.626 AC: 6624 AN: 10576

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43158 AN: 67996

Other (OTH) AF: 0.643 AC: 1359 AN: 2114

Alfa AF: 0.639 Hom.: 83194

Bravo AF: 0.649

Asia WGS AF: 0.523 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.0
DANN	Benign	0.85
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2275675; hg19: chr1-183439483;