rs1944627

Variant names:

• chr11-127022318-G-A
• rs1944627
• ENST00000530177.2:n.154+411G>A

Variant summary

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

The ENST00000530177.2(ENSG00000255087):​n.154+411G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,976 control chromosomes in the GnomAD database, including 8,657 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 0.33 (8657 hom., cov: 32)
• Consequence: ENSG00000255087 ENST00000530177.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

ENSG00000255087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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.154+411G>A		intron_variant	Intron 1 of 7	4
ENSG00000255087	ENST00000647195.1	n.143+411G>A		intron_variant	Intron 1 of 9
ENSG00000255087	ENST00000654157.1	n.150+411G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50529 AN: 151858 Hom.: 8635 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.333 AC: 50605 AN: 151976 Hom.: 8657 Cov.: 32 AF XY: 0.337 AC XY: 25045 AN XY: 74260

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.340

Alfa AF: 0.314 Hom.: 3843

Bravo AF: 0.340

Asia WGS AF: 0.409 AC: 1420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1944627; hg19: chr11-126892213;