rs11662010

chr18-77249441-A-G

Variant summary

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

The XR_007066422.1(LOC124904329):n.721T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,942 control chromosomes in the GnomAD database, including 13,483 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 0.42 (13483 hom., cov: 32)
• Consequence: LOC124904329 XR_007066422.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

Genes affected

LOC124904329 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904329	XR_007066422.1	n.721T>C		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63281 AN: 151824 Hom.: 13472 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.417 AC: 63320 AN: 151942 Hom.: 13483 Cov.: 32 AF XY: 0.414 AC XY: 30718 AN XY: 74268

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.419

Alfa AF: 0.442 Hom.: 3543

Bravo AF: 0.412

Asia WGS AF: 0.298 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.2
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11662010; hg19: chr18-74961397;