rs4568943

chr10-102902124-C-Achr10-102902124-C-T

Variant summary

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

The NR_160733.1(LOC107984265):n.169-1614G>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 0.0945 in 152,170 control chromosomes in the GnomAD database, including 882 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 0.095 (882 hom., cov: 32)
• Consequence: LOC107984265 NR_160733.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984265	NR_160733.1	n.169-1614G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652934.1	n.169-1614G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0945 AC: 14364 AN: 152052 Hom.: 877 Cov.: 32

Gnomad AFR AF: 0.0591

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0909

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0945 AC: 14383 AN: 152170 Hom.: 882 Cov.: 32 AF XY: 0.0964 AC XY: 7171 AN XY: 74386

Gnomad4 AFR AF: 0.0592

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.0758

Gnomad4 NFE AF: 0.0909

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0421 Hom.: 36

Bravo AF: 0.0978

Asia WGS AF: 0.200 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.7
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4568943; hg19: chr10-104661881;