rs674237

Variant names:

• chr11-127057517-G-A
• rs674237
• ENST00000530177.2:n.707+3829G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-127057517-G-A
• chr11-127057517-G-C

Variant summary

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

The ENST00000530177.2(ENSG00000255087):​n.707+3829G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,884 control chromosomes in the GnomAD database, including 13,400 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 0.40 (13400 hom., cov: 32)
• Consequence: ENSG00000255087 ENST00000530177.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

ENSG00000255087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255087	ENST00000530177.2	n.707+3829G>A		intron_variant	Intron 3 of 7	4
ENSG00000255087	ENST00000647195.1	n.696+3829G>A		intron_variant	Intron 3 of 9
ENSG00000255087	ENST00000654637.1	n.710+3829G>A		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60769 AN: 151766 Hom.: 13372 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.401 AC: 60853 AN: 151884 Hom.: 13400 Cov.: 32 AF XY: 0.404 AC XY: 29998 AN XY: 74252

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.363

Alfa AF: 0.363 Hom.: 1351

Bravo AF: 0.406

Asia WGS AF: 0.329 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.033
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs674237; hg19: chr11-126927412;