rs7037591

chr9-1347581-T-G

Variant summary

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

The XR_002956872.2(LOC102723803):n.356+36549T>G 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 0.0673 in 152,216 control chromosomes in the GnomAD database, including 408 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 0.067 (408 hom., cov: 33)
• Consequence: LOC102723803 XR_002956872.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534

Genes affected

LOC102723803 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723803	XR_002956872.2	n.356+36549T>G		intron_variant, non_coding_transcript_variant
LOC102723803	XR_929415.3	n.356+36549T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0673 AC: 10239 AN: 152098 Hom.: 405 Cov.: 33

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0563

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0698

Gnomad OTH AF: 0.0899

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

GnomAD4 genome AF: 0.0673 AC: 10248 AN: 152216 Hom.: 408 Cov.: 33 AF XY: 0.0689 AC XY: 5124 AN XY: 74418

Gnomad4 AFR AF: 0.0396

Gnomad4 AMR AF: 0.0566

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0812

Gnomad4 NFE AF: 0.0698

Gnomad4 OTH AF: 0.0889

Alfa AF: 0.0711 Hom.: 379

Bravo AF: 0.0645

Asia WGS AF: 0.152 AC: 526 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	8.3
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7037591; hg19: chr9-1347581;