3-30420911-G-A

Variant names:

• chr3-30420911-G-A
• rs7640543
• XR_940683.2:n.1749C>T

Variant summary

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

The XR_940683.2(LOC105377013):​n.1749C>T 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 0.243 in 151,938 control chromosomes in the GnomAD database, including 5,018 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 0.24 (5018 hom., cov: 31)
• Consequence: LOC105377013 XR_940683.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 23 publications found

Genes affected

LOC105377013 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691186.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289450	ENST00000691186.2		n.281+29023G>A		intron	N/A
	ENSG00000289450	ENST00000701024.2		n.353-15282G>A		intron	N/A
	ENSG00000227549	ENST00000813769.1		n.505+1349C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36895 AN: 151820 Hom.: 5017 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.257

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.243 AC: 36898 AN: 151938 Hom.: 5018 Cov.: 31 AF XY: 0.239 AC XY: 17765 AN XY: 74244

African (AFR) AF: 0.131 AC: 5441 AN: 41454

American (AMR) AF: 0.249 AC: 3790 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1156 AN: 3472

East Asian (EAS) AF: 0.114 AC: 590 AN: 5158

South Asian (SAS) AF: 0.191 AC: 917 AN: 4812

European-Finnish (FIN) AF: 0.256 AC: 2691 AN: 10526

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21440 AN: 67950

Other (OTH) AF: 0.254 AC: 538 AN: 2114

Alfa AF: 0.292 Hom.: 12678

Bravo AF: 0.237

Asia WGS AF: 0.135 AC: 470 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.59
DANN	Benign	0.82
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7640543; hg19: chr3-30462403;