rs10945275

Positions:

• chr6-70958144-C-T

Variant summary

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

The XM_047419611.1(LOC124901229):​c.*786C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,058 control chromosomes in the GnomAD database, including 5,197 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 (5197 hom., cov: 32)
• Consequence: LOC124901229 XM_047419611.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

Genes affected

LOC124901229 (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 = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901229	XM_047419611.1	c.*786C>T		3_prime_UTR_variant	2/2		XP_047275567.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35523 AN: 151940 Hom.: 5190 Cov.: 32

Gnomad AFR AF: 0.0703

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.234 AC: 35536 AN: 152058 Hom.: 5197 Cov.: 32 AF XY: 0.239 AC XY: 17767 AN XY: 74320

Gnomad4 AFR AF: 0.0702

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.238

Alfa AF: 0.241 Hom.: 1003

Bravo AF: 0.209

Asia WGS AF: 0.368 AC: 1282 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	6.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10945275; hg19: chr6-71667847;