rs7003495

chr8-137856449-T-C

Variant summary

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

The NR_161374.1(LOC401478):n.574-18564A>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 0.18 in 152,126 control chromosomes in the GnomAD database, including 2,685 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 0.18 (2685 hom., cov: 32)
• Consequence: LOC401478 NR_161374.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727

Genes affected

(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 (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC401478	NR_161374.1	n.574-18564A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000518973.1	n.515-18564A>G		intron_variant, non_coding_transcript_variant		2
	ENST00000667239.1	n.238-608T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27413 AN: 152008 Hom.: 2677 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0555

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.180 AC: 27447 AN: 152126 Hom.: 2685 Cov.: 32 AF XY: 0.177 AC XY: 13192 AN XY: 74368

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0556

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.208

Alfa AF: 0.214 Hom.: 1715

Bravo AF: 0.175

Asia WGS AF: 0.0890 AC: 310 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	1.3
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7003495; hg19: chr8-138868692;