rs11680911

Positions:

• chr2-127131181-A-C
• chr2-127131181-A-T

Variant summary

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

The XR_923311.4(LOC105373605):​n.846-2057A>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 0.276 in 152,174 control chromosomes in the GnomAD database, including 6,164 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 0.28 (6164 hom., cov: 32)
• Consequence: LOC105373605 XR_923311.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

Genes affected

LOC105373605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373605	XR_923311.4	n.846-2057A>C		intron_variant, non_coding_transcript_variant
LOC105373605	XR_923310.3	n.449-2057A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41887 AN: 152056 Hom.: 6156 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.276 AC: 41941 AN: 152174 Hom.: 6164 Cov.: 32 AF XY: 0.271 AC XY: 20145 AN XY: 74406

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.273

Alfa AF: 0.142 Hom.: 310

Bravo AF: 0.269

Asia WGS AF: 0.167 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11680911; hg19: chr2-127888757;