rs2769965

Positions:

• chr9-79204129-G-A

Variant summary

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

The XR_007061599.1(LOC124902186):​n.201+2722G>A 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 0.406 in 151,944 control chromosomes in the GnomAD database, including 13,257 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 0.41 (13257 hom., cov: 33)
• Consequence: LOC124902186 XR_007061599.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

Genes affected

LOC124902186 (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 = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902186	XR_007061599.1	n.201+2722G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61589 AN: 151826 Hom.: 13250 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.406 AC: 61628 AN: 151944 Hom.: 13257 Cov.: 33 AF XY: 0.407 AC XY: 30239 AN XY: 74254

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.385

Alfa AF: 0.442 Hom.: 3485

Bravo AF: 0.388

Asia WGS AF: 0.482 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2769965; hg19: chr9-81819044;