rs675597

chr9-87937727-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_149022.1(LOC497256):n.362+1172T>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 0.0131 in 113,284 control chromosomes in the GnomAD database, including 410 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 0.013 (410 hom., cov: 17)
• Consequence: LOC497256 NR_149022.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0131 (1482/113284) while in subpopulation AFR AF= 0.0443 (1377/31088). AF 95% confidence interval is 0.0423. There are 410 homozygotes in gnomad4. There are 680 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 411 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC497256	NR_149022.1	n.362+1172T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000685869.1	n.376+1168T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0131 AC: 1482 AN: 113212 Hom.: 411 Cov.: 17

Gnomad AFR AF: 0.0444

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00326

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00272

Gnomad SAS AF: 0.00123

Gnomad FIN AF: 0.000258

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000570

Gnomad OTH AF: 0.0116

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

GnomAD4 genome AF: 0.0131 AC: 1482 AN: 113284 Hom.: 410 Cov.: 17 AF XY: 0.0123 AC XY: 680 AN XY: 55446

Gnomad4 AFR AF: 0.0443

Gnomad4 AMR AF: 0.00326

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00273

Gnomad4 SAS AF: 0.00123

Gnomad4 FIN AF: 0.000258

Gnomad4 NFE AF: 0.000570

Gnomad4 OTH AF: 0.0115

Alfa AF: 0.0111 Hom.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.2
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs675597; hg19: chr9-90552642;