rs2645227

chr10-4035359-A-Gchr10-4035359-A-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+3656A>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 0.253 in 152,100 control chromosomes in the GnomAD database, including 6,793 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 0.25 (6793 hom., cov: 32)
• Consequence: LOC107984195 NR_176060.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984195	NR_176060.1	n.613+3656A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667089.1	n.627+3656A>G		intron_variant, non_coding_transcript_variant
	ENST00000656775.1	n.689+3656A>G		intron_variant, non_coding_transcript_variant
	ENST00000658139.1	n.568+3656A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38413 AN: 151980 Hom.: 6769 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.253 AC: 38498 AN: 152100 Hom.: 6793 Cov.: 32 AF XY: 0.244 AC XY: 18143 AN XY: 74378

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0734

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.247

Alfa AF: 0.216 Hom.: 621

Bravo AF: 0.273

Asia WGS AF: 0.229 AC: 795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.6
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2645227; hg19: chr10-4077551;