rs7618915

Variant names:

• chr3-52245578-G-A
• rs7618915
• ENST00000816527.1:n.134C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-52245578-G-A
• chr3-52245578-G-C
• chr3-52245578-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000816527.1(ENSG00000306261):​n.134C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,784 control chromosomes in the GnomAD database, including 7,247 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 0.30 (7247 hom., cov: 31)
• Consequence: ENSG00000306261 ENST00000816527.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384
• Publications: 50 publications found

Genes affected

ENSG00000306261 (HGNC:):

TWF2 (HGNC:9621): (twinfilin actin binding protein 2) The protein encoded by this gene was identified by its interaction with the catalytic domain of protein kinase C-zeta. The encoded protein contains an actin-binding site and an ATP-binding site. It is most closely related to twinfilin (PTK9), a conserved actin monomer-binding protein. [provided by RefSeq, Jul 2008]

PPM1M (HGNC:26506): (protein phosphatase, Mg2+/Mn2+ dependent 1M) Predicted to enable manganese ion binding activity and phosphoprotein phosphatase activity. Predicted to be involved in protein dephosphorylation. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TWF2-DT (HGNC:55619): (TWF2 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816527.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPM1M	NM_144641.4	MANE Select	c.-247G>A		upstream_gene	N/A	NP_653242.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306261	ENST00000816527.1		n.134C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000306261	ENST00000816528.1		n.91C>T		non_coding_transcript_exon	Exon 1 of 2
	TWF2	ENST00000679296.1		c.-270+1101C>T		intron	N/A	ENSP00000504576.1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46180 AN: 151668 Hom.: 7243 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.327

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.304 AC: 46209 AN: 151784 Hom.: 7247 Cov.: 31 AF XY: 0.305 AC XY: 22609 AN XY: 74166

African (AFR) AF: 0.232 AC: 9613 AN: 41436

American (AMR) AF: 0.307 AC: 4691 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1300 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1830 AN: 5092

South Asian (SAS) AF: 0.289 AC: 1392 AN: 4810

European-Finnish (FIN) AF: 0.352 AC: 3708 AN: 10526

Middle Eastern (MID) AF: 0.326 AC: 94 AN: 288

European-Non Finnish (NFE) AF: 0.334 AC: 22662 AN: 67878

Other (OTH) AF: 0.302 AC: 635 AN: 2104

Alfa AF: 0.327 Hom.: 29984

Bravo AF: 0.299

Asia WGS AF: 0.330 AC: 1146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.94
PhyloP100		0.38
PromoterAI		-0.043	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7618915; hg19: chr3-52279594;