rs7042864

Positions:

• chr9-108110027-C-T

Variant summary

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

The XR_007061722.1(LOC105376214):​n.721-56733G>A 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 0.319 in 152,034 control chromosomes in the GnomAD database, including 8,082 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 0.32 (8082 hom., cov: 32)
• Consequence: LOC105376214 XR_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376214	XR_007061722.1	n.721-56733G>A		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.721-56733G>A		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.721-56733G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48451 AN: 151916 Hom.: 8082 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.319 AC: 48470 AN: 152034 Hom.: 8082 Cov.: 32 AF XY: 0.315 AC XY: 23384 AN XY: 74290

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.0682

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.343

Alfa AF: 0.340 Hom.: 14974

Bravo AF: 0.314

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7042864; hg19: chr9-110872307;