rs10486115

chr7-11255121-A-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, non coding transcript 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: ENST00000421121.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

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 (EAS) allele frequency at 95% confidence interval = 0.265 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
	ENST00000445839.5	n.246+1896A>C		intron_variant, non_coding_transcript_variant		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;