rs7363432

Variant names:

• chr20-37678328-A-G
• rs7363432
• ENST00000373508.2:n.551A>G

Variant summary

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

The ENST00000373508.2(ENSG00000204117):​n.551A>G 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 0.0857 in 152,888 control chromosomes in the GnomAD database, including 721 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 0.086 (720 hom., cov: 32)
  • Exomes 𝑓: 0.089 (1 hom.)
• Consequence: ENSG00000204117 ENST00000373508.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 5 publications found

Genes affected

ENSG00000204117 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100287792	NR_040021.1	n.548A>G		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000204117	ENST00000373508.2	n.551A>G		non_coding_transcript_exon_variant	Exon 2 of 4	2
ENSG00000204117	ENST00000655861.1	n.199-12A>G		intron_variant	Intron 1 of 3
ENSG00000204117	ENST00000815582.1	n.202-12A>G		intron_variant	Intron 1 of 3
ENSG00000204117	ENST00000815583.1	n.65-12A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13045 AN: 152220 Hom.: 720 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.0318

Gnomad FIN AF: 0.0774

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0639

Gnomad OTH AF: 0.0933

GnomAD4 exome AF: 0.0891 AC: 49 AN: 550 Hom.: 1 Cov.: 0 AF XY: 0.0848 AC XY: 29 AN XY: 342

African (AFR) AF: 0.167 AC: 1 AN: 6

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0841 AC: 36 AN: 428

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.104 AC: 10 AN: 96

Other (OTH) AF: 0.00 AC: 0 AN: 14

GnomAD4 genome AF: 0.0857 AC: 13053 AN: 152338 Hom.: 720 Cov.: 32 AF XY: 0.0848 AC XY: 6314 AN XY: 74498

African (AFR) AF: 0.143 AC: 5961 AN: 41576

American (AMR) AF: 0.0702 AC: 1075 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3470

East Asian (EAS) AF: 0.0291 AC: 151 AN: 5188

South Asian (SAS) AF: 0.0321 AC: 155 AN: 4832

European-Finnish (FIN) AF: 0.0774 AC: 822 AN: 10620

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0639 AC: 4349 AN: 68028

Other (OTH) AF: 0.0919 AC: 194 AN: 2112

Alfa AF: 0.0780 Hom.: 108

Bravo AF: 0.0880

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.37
DANN	Benign	0.54
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7363432; hg19: chr20-36306730;