rs679170

Positions:

• chr2-4467182-A-G

Variant summary

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

The ENST00000707165.1(ENSG00000291325):​n.506+16151A>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 0.168 in 152,178 control chromosomes in the GnomAD database, including 2,618 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 (2618 hom., cov: 32)
• Consequence: ENST00000707165.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

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 (SAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000707165.1	n.506+16151A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25517 AN: 152060 Hom.: 2615 Cov.: 32

Gnomad AFR AF: 0.0527

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.168 AC: 25532 AN: 152178 Hom.: 2618 Cov.: 32 AF XY: 0.169 AC XY: 12552 AN XY: 74404

Gnomad4 AFR AF: 0.0526

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.190

Alfa AF: 0.189 Hom.: 493

Bravo AF: 0.169

Asia WGS AF: 0.273 AC: 951 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	1.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs679170; hg19: chr2-4514772;