rs2014307

Positions:

• chr10-122458116-T-G

Variant summary

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

The ENST00000647969.1(ENSG00000285955):​n.182+379A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 151,900 control chromosomes in the GnomAD database, including 30,025 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 0.63 (30025 hom., cov: 31)
• Consequence: ENSG00000285955 ENST00000647969.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

ENSG00000285955 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378525	XR_946382.3	n.1874+379A>C		intron_variant
LOC105378525	XR_946383.3	n.1852+379A>C		intron_variant
LOC105378525	XR_946384.3	n.1601+379A>C		intron_variant
LOC105378525	XR_946385.3	n.1852+379A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285955	ENST00000647969.1	n.182+379A>C		intron_variant
ENSG00000285955	ENST00000650300.1	n.1852+379A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.626 AC: 94974 AN: 151782 Hom.: 29977 Cov.: 31

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.626 AC: 95075 AN: 151900 Hom.: 30025 Cov.: 31 AF XY: 0.621 AC XY: 46092 AN XY: 74226

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.622

Alfa AF: 0.612 Hom.: 58072

Bravo AF: 0.629

Asia WGS AF: 0.672 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	8.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2014307; hg19: chr10-124217632;