3-142930268-C-G

Position:

• chr3-142930268-C-G

Variant summary

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

The NR_038455.1(LOC100507389):​n.223-2937C>G 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 0.369 in 151,970 control chromosomes in the GnomAD database, including 11,199 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 0.37 (11199 hom., cov: 32)
• Consequence: LOC100507389 NR_038455.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100507389	NR_038455.1	n.223-2937C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658594.1	n.196-2937C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55942 AN: 151852 Hom.: 11168 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.369 AC: 56041 AN: 151970 Hom.: 11199 Cov.: 32 AF XY: 0.363 AC XY: 26929 AN XY: 74228

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.364

Alfa AF: 0.316 Hom.: 4179

Bravo AF: 0.376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.016
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9832727; hg19: chr3-142649110;