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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901750	XR_007060537.1	n.29222-25659T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299028	ENST00000759933.1	n.988T>G		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs10435419; hg19: chr7-134330359;