chr11-127057517-G-A

Position:

• chr11-127057517-G-A

Variant summary

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

The ENST00000647195.1(ENSG00000255087):​n.696+3829G>A 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 0.401 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: ENST00000647195.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000647195.1	n.696+3829G>A		intron_variant, non_coding_transcript_variant

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;