rs638300

chr11-106374741-G-A

Variant summary

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

The XR_947985.1(LOC105369474):n.101+5485G>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 0.379 in 152,004 control chromosomes in the GnomAD database, including 15,579 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 0.38 (15579 hom., cov: 32)
• Consequence: LOC105369474 XR_947985.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

Genes affected

LOC105369474 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369474	XR_947985.1	n.101+5485G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57436 AN: 151886 Hom.: 15520 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.379 AC: 57549 AN: 152004 Hom.: 15579 Cov.: 32 AF XY: 0.371 AC XY: 27555 AN XY: 74308

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.387

Alfa AF: 0.267 Hom.: 6089

Bravo AF: 0.401

Asia WGS AF: 0.242 AC: 844 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.3
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs638300; hg19: chr11-106245468;