rs6945912

chr7-31168632-C-T

Variant summary

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

The XR_001745159.1(LOC107986781):n.256+30943C>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 0.0543 in 152,056 control chromosomes in the GnomAD database, including 635 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 0.054 (635 hom., cov: 32)
• Consequence: LOC107986781 XR_001745159.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

Genes affected

LOC107986781 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986781	XR_001745159.1	n.256+30943C>T		intron_variant, non_coding_transcript_variant
LOC107986781	XR_001745160.2	n.257-26977C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0543 AC: 8254 AN: 151938 Hom.: 637 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0197

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0451

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.00577

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00293

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0543 AC: 8263 AN: 152056 Hom.: 635 Cov.: 32 AF XY: 0.0530 AC XY: 3939 AN XY: 74350

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0196

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0452

Gnomad4 SAS AF: 0.0286

Gnomad4 FIN AF: 0.00577

Gnomad4 NFE AF: 0.00293

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0331 Hom.: 49

Bravo AF: 0.0611

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.1
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6945912; hg19: chr7-31208246;