8-137893053-A-G

Position:

• chr8-137893053-A-G

Variant summary

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

The NR_161374.1(LOC401478):​n.574-55168T>C 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 0.739 in 152,058 control chromosomes in the GnomAD database, including 44,409 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 0.74 (44409 hom., cov: 31)
• Consequence: LOC401478 NR_161374.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC401478	NR_161374.1	n.574-55168T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000518973.1	n.515-55168T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000667239.1	n.301-35628A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112220 AN: 151940 Hom.: 44385 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.739 AC: 112296 AN: 152058 Hom.: 44409 Cov.: 31 AF XY: 0.742 AC XY: 55134 AN XY: 74312

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.820

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.870

Gnomad4 OTH AF: 0.744

Alfa AF: 0.851 Hom.: 60130

Bravo AF: 0.718

Asia WGS AF: 0.819 AC: 2850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9657451; hg19: chr8-138905296;