10-121470112-T-G

Variant names:

• chr10-121470112-T-G
• rs2420941
• ENST00000841803.1:n.121-48A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000841803.1(ENSG00000309510):​n.121-48A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,104 control chromosomes in the GnomAD database, including 12,220 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 0.37 (12220 hom., cov: 33)
• Consequence: ENSG00000309510 ENST00000841803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.804
• Publications: 9 publications found

Genes affected

ENSG00000309510 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841803.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309510	ENST00000841803.1		n.121-48A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56577 AN: 151984 Hom.: 12220 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.372 AC: 56601 AN: 152104 Hom.: 12220 Cov.: 33 AF XY: 0.372 AC XY: 27678 AN XY: 74352

African (AFR) AF: 0.143 AC: 5953 AN: 41510

American (AMR) AF: 0.343 AC: 5242 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1646 AN: 3472

East Asian (EAS) AF: 0.387 AC: 1998 AN: 5164

South Asian (SAS) AF: 0.427 AC: 2060 AN: 4820

European-Finnish (FIN) AF: 0.430 AC: 4546 AN: 10566

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.496 AC: 33717 AN: 67988

Other (OTH) AF: 0.414 AC: 872 AN: 2106

Alfa AF: 0.447 Hom.: 28317

Bravo AF: 0.354

Asia WGS AF: 0.349 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.35
PhyloP100		-0.80

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2420941;

hg19: chr10-123229626;