rs1407846

Positions:

• chr9-108383173-G-C

Variant summary

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

The XR_007061722.1(LOC105376214):​n.326-7577C>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 0.0519 in 152,248 control chromosomes in the GnomAD database, including 336 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 0.052 (336 hom., cov: 32)
• Consequence: LOC105376214 XR_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0998 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376214	XR_007061722.1	n.326-7577C>G		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.326-7577C>G		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.326-7577C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0518 AC: 7885 AN: 152130 Hom.: 337 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0405

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.0205

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0315

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0519 AC: 7900 AN: 152248 Hom.: 336 Cov.: 32 AF XY: 0.0526 AC XY: 3912 AN XY: 74436

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0404

Gnomad4 ASJ AF: 0.0527

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0765

Gnomad4 FIN AF: 0.0205

Gnomad4 NFE AF: 0.0315

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0411 Hom.: 13

Bravo AF: 0.0538

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1407846; hg19: chr9-111145453;