rs7340793

Positions:

• chr4-34004663-G-C
• chr4-34004663-G-T

Variant summary

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

The NR_125902.1(LOC101928622):​n.60-24377C>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 0.147 in 150,714 control chromosomes in the GnomAD database, including 2,177 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 0.15 (2177 hom., cov: 31)
• Consequence: LOC101928622 NR_125902.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928622	NR_125902.1	n.60-24377C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000505018.1	n.60-24377C>G		intron_variant, non_coding_transcript_variant		1
	ENST00000664054.1	n.80+35172C>G		intron_variant, non_coding_transcript_variant
	ENST00000512581.5	n.48+35172C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22212 AN: 150608 Hom.: 2173 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.126

Gnomad NFE AF: 0.0790

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.147 AC: 22222 AN: 150714 Hom.: 2177 Cov.: 31 AF XY: 0.150 AC XY: 11010 AN XY: 73626

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0757

Gnomad4 NFE AF: 0.0790

Gnomad4 OTH AF: 0.145

Alfa AF: 0.117 Hom.: 183

Bravo AF: 0.160

Asia WGS AF: 0.233 AC: 808 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.43
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7340793; hg19: chr4-34006285;