8-57196661-G-T

Position:

• chr8-57196661-G-T

Variant summary

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

The variant allele was found at a frequency of 0.113 in 152,078 control chromosomes in the GnomAD database, including 1,000 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 0.11 (1000 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57196661G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01606	ENST00000518556.5	n.223+2650G>T		intron_variant		3
LINC01606	ENST00000519241.6	n.558+2650G>T		intron_variant		3
LINC01606	ENST00000519314.5	n.490+2650G>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17101 AN: 151960 Hom.: 995 Cov.: 32

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.0606

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.113 AC: 17123 AN: 152078 Hom.: 1000 Cov.: 32 AF XY: 0.112 AC XY: 8356 AN XY: 74322

Gnomad4 AFR AF: 0.0799

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0720

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.114

Alfa AF: 0.121 Hom.: 130

Bravo AF: 0.109

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.96
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17194995; hg19: chr8-58109220;