rs9363741

Positions:

• chr6-67319148-A-G

Variant summary

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

The XR_942658.3(LOC105377842):​n.431-8325A>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 0.226 in 151,868 control chromosomes in the GnomAD database, including 3,948 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 (3948 hom., cov: 32)
• Consequence: LOC105377842 XR_942658.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505

Genes affected

LOC105377842 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377842	XR_942658.3	n.431-8325A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34252 AN: 151750 Hom.: 3948 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.226 AC: 34272 AN: 151868 Hom.: 3948 Cov.: 32 AF XY: 0.224 AC XY: 16642 AN XY: 74228

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.236

Alfa AF: 0.255 Hom.: 10351

Bravo AF: 0.218

Asia WGS AF: 0.211 AC: 732 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
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: rs9363741; hg19: chr6-68029041; COSMIC: COSV69401513;