ENST00000421121.5:n.113+1896A>C

Variant names:

• chr7-11255121-A-C
• rs10486115
• ENST00000421121.5:n.113+1896A>C

Variant summary

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

The ENST00000421121.5(ENSG00000230333):​n.113+1896A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 152,282 control chromosomes in the GnomAD database, including 350 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 0.031 (350 hom., cov: 32)
• Consequence: ENSG00000230333 ENST00000421121.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

Genes affected

ENSG00000230333 (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 (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230333	ENST00000421121.5	n.113+1896A>C		intron_variant	Intron 1 of 2	1
ENSG00000230333	ENST00000428533.5	n.138+57677A>C		intron_variant	Intron 1 of 2	5
ENSG00000230333	ENST00000428967.5	n.497+6746A>C		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0303 AC: 4618 AN: 152164 Hom.: 343 Cov.: 32

Gnomad AFR AF: 0.00876

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.00770

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0305 AC: 4646 AN: 152282 Hom.: 350 Cov.: 32 AF XY: 0.0348 AC XY: 2595 AN XY: 74464

Gnomad4 AFR AF: 0.00883

Gnomad4 AMR AF: 0.0997

Gnomad4 ASJ AF: 0.00865

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0153

Gnomad4 NFE AF: 0.00772

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.0178 Hom.: 22

Bravo AF: 0.0352

Asia WGS AF: 0.181 AC: 626 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486115; hg19: chr7-11294748;