rs10435419

Variant names:

• chr7-134645607-A-C
• rs10435419
• ENST00000759933.1:n.988T>G

Variant summary

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

The ENST00000759933.1(ENSG00000299028):​n.988T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0284 in 152,308 control chromosomes in the GnomAD database, including 94 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 0.028 (94 hom., cov: 33)
• Consequence: ENSG00000299028 ENST00000759933.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 2 publications found

Genes affected

ENSG00000299028 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759933.1. 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
	ENSG00000299028	ENST00000759933.1		n.988T>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0284 AC: 4319 AN: 152190 Hom.: 90 Cov.: 33

Gnomad AFR AF: 0.0246

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0489

Gnomad FIN AF: 0.0140

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0209

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0284 AC: 4325 AN: 152308 Hom.: 94 Cov.: 33 AF XY: 0.0293 AC XY: 2179 AN XY: 74470

African (AFR) AF: 0.0246 AC: 1021 AN: 41564

American (AMR) AF: 0.0519 AC: 795 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3472

East Asian (EAS) AF: 0.111 AC: 577 AN: 5180

South Asian (SAS) AF: 0.0481 AC: 232 AN: 4824

European-Finnish (FIN) AF: 0.0140 AC: 149 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0209 AC: 1423 AN: 68026

Other (OTH) AF: 0.0355 AC: 75 AN: 2114

Alfa AF: 0.0323 Hom.: 74

Bravo AF: 0.0339

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		0.092

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: rs10435419;

hg19: chr7-134330359;