rs4636294

chr9-21747804-A-Gchr9-21747804-A-T

Variant summary

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

The XR_001746563.3(LOC107987026):n.163+20021T>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 0.6 in 151,812 control chromosomes in the GnomAD database, including 28,560 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 0.60 (28560 hom., cov: 31)
• Consequence: LOC107987026 XR_001746563.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263

Genes affected

LOC107987026 (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 (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987026	XR_001746563.3	n.163+20021T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.600 AC: 90984 AN: 151694 Hom.: 28505 Cov.: 31

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.600 AC: 91107 AN: 151812 Hom.: 28560 Cov.: 31 AF XY: 0.595 AC XY: 44115 AN XY: 74204

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.569

Alfa AF: 0.529 Hom.: 44706

Bravo AF: 0.623

Asia WGS AF: 0.536 AC: 1863 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.7
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4636294; hg19: chr9-21747803;