rs9320841

Positions:

• chr6-121793305-A-G
• chr6-121793305-A-T

Variant summary

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

The XR_942936.3(LOC105377979):​n.237+25690A>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 0.231 in 152,092 control chromosomes in the GnomAD database, including 6,782 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 0.23 (6782 hom., cov: 32)
• Consequence: LOC105377979 XR_942936.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

Genes affected

LOC105377979 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377979	XR_942936.3	n.237+25690A>G		intron_variant, non_coding_transcript_variant
LOC105377979	XR_942937.4	n.237+25690A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.230 AC: 35021 AN: 151974 Hom.: 6744 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0977

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0999

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.231 AC: 35106 AN: 152092 Hom.: 6782 Cov.: 32 AF XY: 0.229 AC XY: 17055 AN XY: 74338

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0977

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0998

Gnomad4 OTH AF: 0.201

Alfa AF: 0.0890 Hom.: 207

Bravo AF: 0.244

Asia WGS AF: 0.298 AC: 1035 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9320841; hg19: chr6-122114451;