rs4910907

Positions:

• chr11-4147621-G-A
• chr11-4147621-G-T

Variant summary

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

The ENST00000641518.1(ENSG00000293433):​n.1093C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 152,228 control chromosomes in the GnomAD database, including 59,949 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 0.89 (59948 hom., cov: 33)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: ENST00000641518.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.925 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
	ENST00000641518.1	n.1093C>T		non_coding_transcript_exon_variant	2/2
	ENST00000641245.1	n.51-284C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134757 AN: 152106 Hom.: 59942 Cov.: 33

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.884

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.886 AC: 134804 AN: 152224 Hom.: 59948 Cov.: 33 AF XY: 0.881 AC XY: 65576 AN XY: 74414

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.877

Alfa AF: 0.920 Hom.: 29333

Bravo AF: 0.877

Asia WGS AF: 0.789 AC: 2745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4910907; hg19: chr11-4168851;