rs11582200

Positions:

• chr1-29669033-C-A

Variant summary

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

The XR_001737957.1(LOC107984934):​n.221-10086C>A 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 0.179 in 152,094 control chromosomes in the GnomAD database, including 2,509 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 0.18 (2509 hom., cov: 31)
• Consequence: LOC107984934 XR_001737957.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

LOC107984934 (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 (SAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984934	XR_001737957.1	n.221-10086C>A		intron_variant, non_coding_transcript_variant
LOC107984934	XR_001737956.1	n.221-10086C>A		intron_variant, non_coding_transcript_variant
LOC107984934	XR_001737958.2	n.221-10086C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27217 AN: 151976 Hom.: 2507 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.179 AC: 27241 AN: 152094 Hom.: 2509 Cov.: 31 AF XY: 0.180 AC XY: 13366 AN XY: 74358

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.194

Alfa AF: 0.194 Hom.: 1424

Bravo AF: 0.176

Asia WGS AF: 0.269 AC: 937 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	0.0050
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11582200; hg19: chr1-30141880; COSMIC: COSV59933904;