rs7867029

Positions:

• chr9-78405502-G-C

Variant summary

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

The XR_001746759.2(LOC107987083):​n.1049-16592G>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 0.215 in 152,158 control chromosomes in the GnomAD database, including 4,776 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 0.21 (4776 hom., cov: 32)
• Consequence: LOC107987083 XR_001746759.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

Genes affected

LOC107987083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987083	XR_001746759.2	n.1049-16592G>C		intron_variant, non_coding_transcript_variant
LOC107987083	XR_001746760.2	n.1049-16592G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32600 AN: 152040 Hom.: 4760 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0822

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.215 AC: 32650 AN: 152158 Hom.: 4776 Cov.: 32 AF XY: 0.212 AC XY: 15753 AN XY: 74404

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.0822

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.199

Alfa AF: 0.166 Hom.: 391

Bravo AF: 0.233

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7867029; hg19: chr9-81020418;