rs11685593

Positions:

• chr2-127130545-C-T

Variant summary

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

The XR_923311.4(LOC105373605):​n.846-2693C>T 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 0.139 in 151,854 control chromosomes in the GnomAD database, including 1,724 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 0.14 (1724 hom., cov: 31)
• Consequence: LOC105373605 XR_923311.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566

Genes affected

LOC105373605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373605	XR_923311.4	n.846-2693C>T		intron_variant, non_coding_transcript_variant
LOC105373605	XR_923310.3	n.449-2693C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21039 AN: 151736 Hom.: 1718 Cov.: 31

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0631

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.139 AC: 21057 AN: 151854 Hom.: 1724 Cov.: 31 AF XY: 0.137 AC XY: 10168 AN XY: 74208

Gnomad4 AFR AF: 0.0602

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.0646

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.142

Alfa AF: 0.167 Hom.: 1002

Bravo AF: 0.135

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11685593; hg19: chr2-127888121;