rs1886946

Positions:

• chr10-4033464-T-C

Variant summary

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

The NR_176060.1(LOC107984195):​n.613+1761T>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 0.458 in 151,872 control chromosomes in the GnomAD database, including 18,131 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 0.46 (18131 hom., cov: 31)
• Consequence: LOC107984195 NR_176060.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984195	NR_176060.1	n.613+1761T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000667089.1	n.627+1761T>C		intron_variant, non_coding_transcript_variant
	ENST00000660544.1	n.866T>C		non_coding_transcript_exon_variant	2/2
	ENST00000656775.1	n.689+1761T>C		intron_variant, non_coding_transcript_variant
	ENST00000658139.1	n.568+1761T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69480 AN: 151754 Hom.: 18091 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.458 AC: 69578 AN: 151872 Hom.: 18131 Cov.: 31 AF XY: 0.446 AC XY: 33131 AN XY: 74224

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.478

Alfa AF: 0.394 Hom.: 19751

Bravo AF: 0.480

Asia WGS AF: 0.365 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1886946; hg19: chr10-4075656;