rs11903376

chr2-225819270-C-T

Variant summary

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

The XR_001739907.2(LOC107985992):n.98+48600C>T 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 0.221 in 151,600 control chromosomes in the GnomAD database, including 10,726 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 0.22 (10726 hom., cov: 32)
• Consequence: LOC107985992 XR_001739907.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

Genes affected

LOC107985992 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985992	XR_001739907.2	n.98+48600C>T		intron_variant, non_coding_transcript_variant
LOC105373914	XR_007088108.1	n.254+66387G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33391 AN: 151482 Hom.: 10686 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.00936

Gnomad FIN AF: 0.00617

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.00686

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.221 AC: 33487 AN: 151600 Hom.: 10726 Cov.: 32 AF XY: 0.216 AC XY: 15993 AN XY: 74076

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0257

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.00854

Gnomad4 FIN AF: 0.00617

Gnomad4 NFE AF: 0.00686

Gnomad4 OTH AF: 0.162

Alfa AF: 0.0449 Hom.: 3209

Bravo AF: 0.256

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.71
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11903376; hg19: chr2-226683986;