rs9320784

Positions:

• chr6-120971903-T-C

Variant summary

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

The XR_942934.2(LOC105377977):​n.995-478A>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 0.128 in 151,572 control chromosomes in the GnomAD database, including 1,615 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 0.13 (1615 hom., cov: 32)
• Consequence: LOC105377977 XR_942934.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

Genes affected

LOC105377977 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377977	XR_942934.2	n.995-478A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19389 AN: 151454 Hom.: 1614 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0882

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.128 AC: 19414 AN: 151572 Hom.: 1615 Cov.: 32 AF XY: 0.127 AC XY: 9438 AN XY: 74128

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.0757

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.0559

Gnomad4 NFE AF: 0.0882

Gnomad4 OTH AF: 0.130

Alfa AF: 0.114 Hom.: 231

Bravo AF: 0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
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: rs9320784; hg19: chr6-121293049;