chr4-40043473-C-A

Variant names:

• chr4-40043473-C-A
• rs17511578
• ENST00000381811.2:n.1057G>T

Variant summary

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

The ENST00000381811.2(ENSG00000293349):​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: ENSG00000293349 ENST00000381811.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.12
• Publications: 8 publications found

Genes affected

ENSG00000293349 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC344967	NR_027277.2	n.1057G>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293349	ENST00000381811.2	n.1057G>T		non_coding_transcript_exon_variant	Exon 3 of 3	2
ENSG00000205794	ENST00000507914.2	n.663G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

GnomAD2 exomes AF: 0.0552 AC: 11415 AN: 206632 AF XY: 0.0561

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 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

African (AFR) AF: 0.0256 AC: 720 AN: 28150

American (AMR) AF: 0.0293 AC: 1141 AN: 38876

Ashkenazi Jewish (ASJ) AF: 0.0540 AC: 1296 AN: 23990

East Asian (EAS) AF: 0.0270 AC: 1006 AN: 37304

South Asian (SAS) AF: 0.0653 AC: 5098 AN: 78038

European-Finnish (FIN) AF: 0.0821 AC: 4113 AN: 50110

Middle Eastern (MID) AF: 0.0367 AC: 195 AN: 5318

European-Non Finnish (NFE) AF: 0.0621 AC: 54449 AN: 877178

Other (OTH) AF: 0.0566 AC: 2899 AN: 51216

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

African (AFR) AF: 0.0278 AC: 1155 AN: 41558

American (AMR) AF: 0.0289 AC: 442 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3470

East Asian (EAS) AF: 0.0333 AC: 172 AN: 5160

South Asian (SAS) AF: 0.0624 AC: 301 AN: 4824

European-Finnish (FIN) AF: 0.0802 AC: 851 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0643 AC: 4371 AN: 68002

Other (OTH) AF: 0.0442 AC: 93 AN: 2106

Alfa AF: 0.0587 Hom.: 416

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
PhyloP100		4.1

Splicing

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

Other links and lift over

dbSNP: rs17511578; hg19: chr4-40045093;