3-164660905-C-G

Variant summary

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

The ENST00000702159.1(ENSG00000289884):n.484-26723C>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 0.527 in 151,888 control chromosomes in the GnomAD database, including 21,880 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 0.53 (21880 hom., cov: 32)
• Consequence: ENST00000702159.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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 (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374191	XR_001740998.2	n.484-26723C>G		intron_variant, non_coding_transcript_variant
LOC105374191	XR_001740999.3	n.484-21578C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000702159.1	n.484-26723C>G		intron_variant, non_coding_transcript_variant
	ENST00000701346.1	n.608-26723C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79923 AN: 151772 Hom.: 21850 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.527 AC: 80001 AN: 151888 Hom.: 21880 Cov.: 32 AF XY: 0.527 AC XY: 39098 AN XY: 74212

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.498

Alfa AF: 0.356 Hom.: 952

Bravo AF: 0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.20
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2643191; hg19: chr3-164378693;