8-137868892-C-T

Variant summary

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

The NR_161374.1(LOC401478):n.574-31007G>A 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 0.871 in 152,150 control chromosomes in the GnomAD database, including 58,442 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 0.87 (58442 hom., cov: 32)
• Consequence: LOC401478 NR_161374.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC401478	NR_161374.1	n.574-31007G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000518973.1	n.515-31007G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000667239.1	n.300+11773C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132453 AN: 152032 Hom.: 58390 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.871 AC: 132560 AN: 152150 Hom.: 58442 Cov.: 32 AF XY: 0.874 AC XY: 65013 AN XY: 74382

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.936

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.875

Alfa AF: 0.898 Hom.: 9704

Bravo AF: 0.861

Asia WGS AF: 0.913 AC: 3173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.67
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1877332; hg19: chr8-138881135;