rs574383

Positions:

• chr11-118702959-T-C

Variant summary

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

The XR_007062909.1(LOC105369519):​n.252-1649T>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 0.34 in 151,936 control chromosomes in the GnomAD database, including 9,133 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 0.34 (9133 hom., cov: 31)
• Consequence: LOC105369519 XR_007062909.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466

Genes affected

LOC105369519 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369519	XR_007062909.1	n.252-1649T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000646572.2	n.230-1649T>C		intron_variant, non_coding_transcript_variant
	ENST00000702882.1	n.230-1720T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51613 AN: 151818 Hom.: 9116 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.340 AC: 51676 AN: 151936 Hom.: 9133 Cov.: 31 AF XY: 0.339 AC XY: 25134 AN XY: 74244

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.345

Alfa AF: 0.336 Hom.: 1110

Bravo AF: 0.360

Asia WGS AF: 0.283 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs574383; hg19: chr11-118573668;