rs705469

Positions:

• chr10-3616727-T-C

Variant summary

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

The NR_131187.1(LOC105376360):​n.163-131961T>C 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 0.344 in 146,982 control chromosomes in the GnomAD database, including 8,860 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 0.34 (8860 hom., cov: 24)
• Consequence: LOC105376360 NR_131187.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

Genes affected

LOC105376360 (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 = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376360	NR_131187.1	n.163-131961T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.344 AC: 50518 AN: 146894 Hom.: 8862 Cov.: 24

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.344 AC: 50509 AN: 146982 Hom.: 8860 Cov.: 24 AF XY: 0.337 AC XY: 24060 AN XY: 71442

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.354

Alfa AF: 0.355 Hom.: 1226

Bravo AF: 0.355

Asia WGS AF: 0.242 AC: 835 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs705469; hg19: chr10-3658919;