10-120979038-G-T

Position:

• chr10-120979038-G-T

Variant summary

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

The ENST00000414774.1(ENSG00000227307):​n.49+1614C>A 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 0.387 in 152,006 control chromosomes in the GnomAD database, including 11,991 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 0.39 (11991 hom., cov: 33)
• Consequence: ENST00000414774.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378519	XR_001747609.2	n.540+1614C>A		intron_variant, non_coding_transcript_variant
LOC105378519	XR_946372.3	n.73+1614C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000414774.1	n.49+1614C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58824 AN: 151888 Hom.: 11989 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.387 AC: 58855 AN: 152006 Hom.: 11991 Cov.: 33 AF XY: 0.383 AC XY: 28453 AN XY: 74312

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.384

Alfa AF: 0.425 Hom.: 3899

Bravo AF: 0.389

Asia WGS AF: 0.277 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0080
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11199686; hg19: chr10-122738551;