rs2206416

chr20-41932203-T-C

Variant summary

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

The XR_001754611.2(LOC101927182):n.252+28104T>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 0.369 in 152,050 control chromosomes in the GnomAD database, including 10,848 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 0.37 (10848 hom., cov: 33)
• Consequence: LOC101927182 XR_001754611.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

Genes affected

LOC101927182 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927182	XR_001754611.2	n.252+28104T>C		intron_variant, non_coding_transcript_variant
LOC101927182	XR_001754609.2	n.247+28108T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56122 AN: 151932 Hom.: 10839 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.369 AC: 56157 AN: 152050 Hom.: 10848 Cov.: 33 AF XY: 0.375 AC XY: 27880 AN XY: 74290

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.377

Alfa AF: 0.374 Hom.: 1376

Bravo AF: 0.364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.9
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2206416; hg19: chr20-40560843;