rs959127

Positions:

• chr10-111851811-A-G

Variant summary

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

The ENST00000656217.1(ENSG00000287231):​n.133-62707T>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 0.462 in 152,014 control chromosomes in the GnomAD database, including 18,542 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 (18542 hom., cov: 32)
• Consequence: ENST00000656217.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656217.1	n.133-62707T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70149 AN: 151896 Hom.: 18490 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.462 AC: 70265 AN: 152014 Hom.: 18542 Cov.: 32 AF XY: 0.451 AC XY: 33525 AN XY: 74280

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.412

Alfa AF: 0.390 Hom.: 24969

Bravo AF: 0.477

Asia WGS AF: 0.237 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
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: rs959127; hg19: chr10-113611569;