rs7690426

chr4-114462951-C-T

Variant summary

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

The XR_001741520.3(LOC105377379):n.282+3572C>T 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 0.409 in 152,024 control chromosomes in the GnomAD database, including 14,686 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 0.41 (14686 hom., cov: 33)
• Consequence: LOC105377379 XR_001741520.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

Genes affected

LOC105377379 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377379	XR_001741520.3	n.282+3572C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62261 AN: 151904 Hom.: 14692 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.409 AC: 62241 AN: 152024 Hom.: 14686 Cov.: 33 AF XY: 0.408 AC XY: 30351 AN XY: 74302

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.420

Alfa AF: 0.470 Hom.: 5373

Bravo AF: 0.399

Asia WGS AF: 0.471 AC: 1633 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7690426; hg19: chr4-115384107;