rs16992204

chr21-34738904-T-C

Variant summary

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

The XR_001755016.1(LOC107985515):n.243+1417T>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 0.0256 in 152,318 control chromosomes in the GnomAD database, including 149 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 0.026 (149 hom., cov: 32)
• Consequence: LOC107985515 XR_001755016.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692

Genes affected

LOC107985515 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985515	XR_001755016.1	n.243+1417T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0256 AC: 3893 AN: 152200 Hom.: 149 Cov.: 32

Gnomad AFR AF: 0.0578

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0236

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00119

Gnomad OTH AF: 0.0229

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

GnomAD4 genome AF: 0.0256 AC: 3898 AN: 152318 Hom.: 149 Cov.: 32 AF XY: 0.0266 AC XY: 1978 AN XY: 74480

Gnomad4 AFR AF: 0.0580

Gnomad4 AMR AF: 0.0234

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0163

Gnomad4 NFE AF: 0.00119

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0117 Hom.: 15

Bravo AF: 0.0277

Asia WGS AF: 0.0880 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.0
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16992204; hg19: chr21-36111201;