rs1943482

Positions:

• chr11-57228135-A-G

Variant summary

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

The XR_007062670.1(LOC105369309):​n.1007+1323T>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 0.303 in 152,058 control chromosomes in the GnomAD database, including 8,172 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 0.30 (8172 hom., cov: 32)
• Consequence: LOC105369309 XR_007062670.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

Genes affected

LOC105369309 (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 (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369309	XR_007062670.1	n.1007+1323T>C		intron_variant, non_coding_transcript_variant
LOC105369309	XR_001748217.1	n.1007+1323T>C		intron_variant, non_coding_transcript_variant
LOC105369309	XR_007062671.1	n.1007+1323T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46023 AN: 151940 Hom.: 8160 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.303 AC: 46060 AN: 152058 Hom.: 8172 Cov.: 32 AF XY: 0.314 AC XY: 23340 AN XY: 74334

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.333

Alfa AF: 0.288 Hom.: 1034

Bravo AF: 0.286

Asia WGS AF: 0.505 AC: 1753 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	7.0
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1943482; hg19: chr11-56995609;