rs11127336

chr2-2770197-T-C

Variant summary

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

The ENST00000652954.1(ENSG00000237720):n.105-53648A>G 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 0.937 in 152,298 control chromosomes in the GnomAD database, including 67,040 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 0.94 (67040 hom., cov: 33)
• Consequence: ENST00000652954.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652954.1	n.105-53648A>G		intron_variant, non_coding_transcript_variant
	ENST00000660883.1	n.146-53648A>G		intron_variant, non_coding_transcript_variant
	ENST00000671195.1	n.410-35599A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.937 AC: 142630 AN: 152180 Hom.: 66997 Cov.: 33

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.931

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

GnomAD4 genome AF: 0.937 AC: 142732 AN: 152298 Hom.: 67040 Cov.: 33 AF XY: 0.938 AC XY: 69826 AN XY: 74478

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.918

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.970

Gnomad4 OTH AF: 0.932

Alfa AF: 0.949 Hom.: 21037

Bravo AF: 0.927

Asia WGS AF: 0.957 AC: 3326 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.46
Dann	Benign	0.10

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11127336; hg19: chr2-2773969;