3-171039196-T-G

Position:

• chr3-171039196-T-G

Variant summary

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

The ENST00000655926.1(ENSG00000286856):​n.292-15616T>G 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 0.192 in 152,194 control chromosomes in the GnomAD database, including 5,149 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 (5149 hom., cov: 32)
• Consequence: ENST00000655926.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000655926.1	n.292-15616T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29105 AN: 152076 Hom.: 5130 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.192 AC: 29163 AN: 152194 Hom.: 5149 Cov.: 32 AF XY: 0.187 AC XY: 13935 AN XY: 74434

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0343

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0322

Gnomad4 NFE AF: 0.0836

Gnomad4 OTH AF: 0.168

Alfa AF: 0.112 Hom.: 961

Bravo AF: 0.210

Asia WGS AF: 0.109 AC: 381 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	4.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6785233; hg19: chr3-170756985;