4-40043473-C-A

Position:

• chr4-40043473-C-A

Variant summary

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

The NR_027277.2(LOC344967):​n.1057G>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0586 in 1,342,410 control chromosomes in the GnomAD database, including 2,522 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 0.051 (228 hom., cov: 31)
  • Exomes 𝑓: 0.060 (2294 hom.)
• Consequence: LOC344967 NR_027277.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC344967	NR_027277.2	n.1057G>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000381811.2	n.1057G>T		non_coding_transcript_exon_variant	3/3	2
	ENST00000507914.2	n.663G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7731 AN: 152112 Hom.: 228 Cov.: 31

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0289

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.0331

Gnomad SAS AF: 0.0623

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0642

Gnomad OTH AF: 0.0446

GnomAD3 exomes AF: 0.0552 AC: 11415 AN: 206632 Hom.: 348 AF XY: 0.0561 AC XY: 6202 AN XY: 110634

Gnomad AFR exome AF: 0.0281

Gnomad AMR exome AF: 0.0278

Gnomad ASJ exome AF: 0.0560

Gnomad EAS exome AF: 0.0327

Gnomad SAS exome AF: 0.0650

Gnomad FIN exome AF: 0.0840

Gnomad NFE exome AF: 0.0626

Gnomad OTH exome AF: 0.0576

GnomAD4 exome AF: 0.0596 AC: 70917 AN: 1190180 Hom.: 2294 Cov.: 18 AF XY: 0.0600 AC XY: 36034 AN XY: 600506

Gnomad4 AFR exome AF: 0.0256

Gnomad4 AMR exome AF: 0.0293

Gnomad4 ASJ exome AF: 0.0540

Gnomad4 EAS exome AF: 0.0270

Gnomad4 SAS exome AF: 0.0653

Gnomad4 FIN exome AF: 0.0821

Gnomad4 NFE exome AF: 0.0621

Gnomad4 OTH exome AF: 0.0566

GnomAD4 genome AF: 0.0508 AC: 7735 AN: 152230 Hom.: 228 Cov.: 31 AF XY: 0.0514 AC XY: 3825 AN XY: 74418

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.0289

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.0333

Gnomad4 SAS AF: 0.0624

Gnomad4 FIN AF: 0.0802

Gnomad4 NFE AF: 0.0643

Gnomad4 OTH AF: 0.0442

Alfa AF: 0.0597 Hom.: 89

Bravo AF: 0.0448

Asia WGS AF: 0.0390 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	8.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17511578; hg19: chr4-40045093;