rs2009867

Variant names:

• chr11-61447877-C-A
• rs2009867
• ENST00000541135.5:c.377+9757C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-61447877-C-A
• chr11-61447877-C-T

Variant summary

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

The ENST00000541135.5(ENSG00000256591):​c.377+9757C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 152,278 control chromosomes in the GnomAD database, including 316 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 0.037 (316 hom., cov: 33)
• Consequence: ENSG00000256591 ENST00000541135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.482

Genes affected

ENSG00000256591 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 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
ENSG00000256591	ENST00000541135.5	c.377+9757C>A		intron_variant	Intron 3 of 4	4		ENSP00000443130.1

Frequencies

GnomAD3 genomes AF: 0.0370 AC: 5635 AN: 152160 Hom.: 313 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0143

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.00365

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.000566

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00414

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0371 AC: 5645 AN: 152278 Hom.: 316 Cov.: 33 AF XY: 0.0369 AC XY: 2748 AN XY: 74454

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0142

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.00366

Gnomad4 SAS AF: 0.0296

Gnomad4 FIN AF: 0.000566

Gnomad4 NFE AF: 0.00415

Gnomad4 OTH AF: 0.0236

Alfa AF: 0.00489 Hom.: 1

Bravo AF: 0.0408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2009867; hg19: chr11-61215349;