rs17637161

chr8-137859170-A-Gchr8-137859170-A-T

Variant summary

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

The NR_161374.1(LOC401478):n.574-21285T>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 0.173 in 152,062 control chromosomes in the GnomAD database, including 2,560 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 0.17 (2560 hom., cov: 32)
• Consequence: LOC401478 NR_161374.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC401478	NR_161374.1	n.574-21285T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000518973.1	n.515-21285T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000667239.1	n.300+2051A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26314 AN: 151946 Hom.: 2552 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0555

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.173 AC: 26344 AN: 152062 Hom.: 2560 Cov.: 32 AF XY: 0.170 AC XY: 12650 AN XY: 74322

Gnomad4 AFR AF: 0.0963

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0556

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.201

Alfa AF: 0.199 Hom.: 551

Bravo AF: 0.167

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.7
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17637161; hg19: chr8-138871413;