rs7678151

Positions:

• chr4-4931098-A-G
• chr4-4931098-A-T

Variant summary

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

The NR_125893.1(LOC101928306):​n.354-2722A>G 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 0.69 in 151,972 control chromosomes in the GnomAD database, including 36,609 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 0.69 (36609 hom., cov: 31)
• Consequence: LOC101928306 NR_125893.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

Genes affected

LOC101928306 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928306	NR_125893.1	n.354-2722A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104785 AN: 151854 Hom.: 36548 Cov.: 31

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.690 AC: 104901 AN: 151972 Hom.: 36609 Cov.: 31 AF XY: 0.700 AC XY: 51973 AN XY: 74276

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.688

Alfa AF: 0.665 Hom.: 39124

Bravo AF: 0.695

Asia WGS AF: 0.817 AC: 2837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7678151; hg19: chr4-4932825;