rs16927557

chr9-1325179-A-Gchr9-1325179-A-T

Variant summary

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

The XR_002956872.2(LOC102723803):n.356+14147A>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 0.182 in 152,234 control chromosomes in the GnomAD database, including 3,818 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 0.18 (3818 hom., cov: 33)
• Consequence: LOC102723803 XR_002956872.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

Genes affected

LOC102723803 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723803	XR_002956872.2	n.356+14147A>G		intron_variant, non_coding_transcript_variant
LOC102723803	XR_428436.4	n.357-1895A>G		intron_variant, non_coding_transcript_variant
LOC102723803	XR_929415.3	n.356+14147A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27716 AN: 152116 Hom.: 3802 Cov.: 33

Gnomad AFR AF: 0.0780

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.182 AC: 27739 AN: 152234 Hom.: 3818 Cov.: 33 AF XY: 0.193 AC XY: 14375 AN XY: 74428

Gnomad4 AFR AF: 0.0778

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.179

Alfa AF: 0.184 Hom.: 5012

Bravo AF: 0.187

Asia WGS AF: 0.396 AC: 1372 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	10
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16927557; hg19: chr9-1325179;