rs10249671

Positions:

• chr7-12508291-C-T

Variant summary

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

The NM_001386514.1(LOC102725191):​c.3+3745C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,834 control chromosomes in the GnomAD database, including 7,164 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 0.29 (7164 hom., cov: 32)
• Consequence: LOC102725191 NM_001386514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

Genes affected

LOC102725191 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102725191	NM_001386514.1	c.3+3745C>T		intron_variant		ENST00000636804.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000636804.2	c.3+3745C>T		intron_variant		5	NM_001386514.1	P2

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44468 AN: 151716 Hom.: 7152 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.293 AC: 44507 AN: 151834 Hom.: 7164 Cov.: 32 AF XY: 0.291 AC XY: 21627 AN XY: 74214

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.247

Alfa AF: 0.254 Hom.: 10426

Bravo AF: 0.292

Asia WGS AF: 0.201 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10249671; hg19: chr7-12547917;