chr11-128316987-T-G

Position:

• chr11-128316987-T-G

Variant summary

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

The XR_007062946.1(LOC124902787):​n.209-12512A>C 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 0.365 in 152,128 control chromosomes in the GnomAD database, including 11,943 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 0.37 (11943 hom., cov: 32)
• Consequence: LOC124902787 XR_007062946.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

Genes affected

LOC124902787 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902787	XR_007062946.1	n.209-12512A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55561 AN: 152010 Hom.: 11940 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.365 AC: 55563 AN: 152128 Hom.: 11943 Cov.: 32 AF XY: 0.360 AC XY: 26745 AN XY: 74346

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.404

Alfa AF: 0.474 Hom.: 35144

Bravo AF: 0.358

Asia WGS AF: 0.325 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10893845; hg19: chr11-128186882;