rs1209926

chr21-38785200-T-C

Variant summary

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

The XR_001755102.2(LOC107985480):n.40+1109T>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 0.657 in 152,162 control chromosomes in the GnomAD database, including 33,320 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 0.66 (33320 hom., cov: 33)
• Consequence: LOC107985480 XR_001755102.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

Genes affected

LOC107985480 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985480	XR_001755102.2	n.40+1109T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99865 AN: 152044 Hom.: 33302 Cov.: 33

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.657 AC: 99938 AN: 152162 Hom.: 33320 Cov.: 33 AF XY: 0.657 AC XY: 48841 AN XY: 74388

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.639

Alfa AF: 0.685 Hom.: 26272

Bravo AF: 0.649

Asia WGS AF: 0.570 AC: 1987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1209926; hg19: chr21-40157124;