rs2935283

Positions:

• chr10-4041651-C-G
• chr10-4041651-C-T

Variant summary

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

The NR_176060.1(LOC107984195):​n.613+9948C>G 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 0.0346 in 152,210 control chromosomes in the GnomAD database, including 250 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 0.035 (250 hom., cov: 32)
• Consequence: LOC107984195 NR_176060.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984195	NR_176060.1	n.613+9948C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667089.1	n.628-9819C>G		intron_variant, non_coding_transcript_variant
	ENST00000656775.1	n.690-5430C>G		intron_variant, non_coding_transcript_variant
	ENST00000658139.1	n.569-5430C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0344 AC: 5229 AN: 152092 Hom.: 244 Cov.: 32

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0174

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0109

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00578

Gnomad OTH AF: 0.0296

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

GnomAD4 genome AF: 0.0346 AC: 5270 AN: 152210 Hom.: 250 Cov.: 32 AF XY: 0.0342 AC XY: 2546 AN XY: 74422

Gnomad4 AFR AF: 0.0813

Gnomad4 AMR AF: 0.0173

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.0203

Gnomad4 FIN AF: 0.0109

Gnomad4 NFE AF: 0.00578

Gnomad4 OTH AF: 0.0326

Alfa AF: 0.00180 Hom.: 0

Bravo AF: 0.0387

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
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: rs2935283; hg19: chr10-4083843;