rs9320784

Variant names:

• chr6-120971903-T-C
• rs9320784
• XR_942934.2:n.995-478A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_942934.2(LOC105377977):​n.995-478A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 1 publications found

Genes affected

LOC105377977 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105377977	XR_942934.2	n.995-478A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.228 AC: 9447 AN: 41372

American (AMR) AF: 0.0757 AC: 1147 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3458

East Asian (EAS) AF: 0.108 AC: 556 AN: 5126

South Asian (SAS) AF: 0.197 AC: 951 AN: 4816

European-Finnish (FIN) AF: 0.0559 AC: 593 AN: 10616

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0882 AC: 5977 AN: 67734

Other (OTH) AF: 0.130 AC: 273 AN: 2096

Alfa AF: 0.118 Hom.: 251

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs9320784; hg19: chr6-121293049;