rs10837120

chr11-39154873-G-C

Variant summary

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

The ENST00000649415.1(ENSG00000285751):n.114+6652C>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 0.577 in 151,834 control chromosomes in the GnomAD database, including 26,163 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 0.58 (26163 hom., cov: 32)
• Consequence: ENST00000649415.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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
	ENST00000649415.1	n.114+6652C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87541 AN: 151716 Hom.: 26149 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.577 AC: 87593 AN: 151834 Hom.: 26163 Cov.: 32 AF XY: 0.580 AC XY: 43046 AN XY: 74158

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.619

Alfa AF: 0.584 Hom.: 3349

Bravo AF: 0.581

Asia WGS AF: 0.725 AC: 2511 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.5
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10837120; hg19: chr11-39176423;