rs9257691

Positions:

• chr6-29301152-C-A
• chr6-29301152-C-G
• chr6-29301152-C-T

Variant summary

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

The XR_926670.1(LOC105375005):​n.220-16192G>T 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 0.419 in 151,952 control chromosomes in the GnomAD database, including 14,650 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 0.42 (14650 hom., cov: 32)
• Consequence: LOC105375005 XR_926670.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422

Genes affected

LOC105375005 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375005	XR_926670.1	n.220-16192G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63669 AN: 151832 Hom.: 14638 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.419 AC: 63685 AN: 151952 Hom.: 14650 Cov.: 32 AF XY: 0.421 AC XY: 31281 AN XY: 74268

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.406

Alfa AF: 0.428 Hom.: 4504

Bravo AF: 0.394

Asia WGS AF: 0.405 AC: 1407 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.059
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9257691; hg19: chr6-29268929;