rs7640543

chr3-30420911-G-Achr3-30420911-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105377013 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377013	XR_940683.2	n.1749C>T		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691186.1	n.212+29023G>A		intron_variant, non_coding_transcript_variant
	ENST00000701024.1	n.213-15282G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.254

Alfa AF: 0.290 Hom.: 8456

Bravo AF: 0.237

Asia WGS AF: 0.135 AC: 470 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.59
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7640543; hg19: chr3-30462403;