8-2738578-G-T

Variant summary

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

The NR_168443.1(LOC105377785):n.538+11085G>T 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 0.186 in 151,956 control chromosomes in the GnomAD database, including 3,307 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 0.19 (3307 hom., cov: 32)
• Consequence: LOC105377785 NR_168443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377785	NR_168443.1	n.538+11085G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654515.1	n.531+11085G>T		intron_variant, non_coding_transcript_variant
	ENST00000520024.1	n.176+11085G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000670600.1	n.538+11085G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28324 AN: 151840 Hom.: 3308 Cov.: 32

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.186 AC: 28317 AN: 151956 Hom.: 3307 Cov.: 32 AF XY: 0.184 AC XY: 13669 AN XY: 74292

Gnomad4 AFR AF: 0.0552

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.200

Alfa AF: 0.242 Hom.: 6941

Bravo AF: 0.175

Asia WGS AF: 0.222 AC: 770 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.1
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17755518; hg19: chr8-2596106;